Alzheimer&#39;s disease secretase, APP substrates therefor, and uses therefor

ABSTRACT

The present invention provides the enzyme and enzymatic procedures for cleaving the β secretase cleavage site of the APP protein and associated nucleic acids, peptides, vectors, cells and cell isolates and assays. The invention further provides a modified APP protein and associated nucleic acids, peptides, vectors, cells, and cell isolates, and assays that are particularly useful for identifying candidate therapeutics for treatment or prevention of Alzheimer&#39;s disease.

The present application is a continuation of U.S. application Ser. No.09/416,901, filed Oct. 13, 1999, now U.S. Pat. No. 6,699,671, whichclaims priority benefit of U.S. Provisional Patent Application No.60/155,493, filed Sep. 23, 1999. The present application also claimspriority benefit as a continuation-in-part of U.S. patent applicationSer. No. 09/404,133 now abandoned and PCT/US99/20881, both filed Sep.23, 1999, both of which in turn claim priority benefit of U.S.Provisional Patent Application No. 60/101,594, filed Sep. 24, 1998. Allof these priority applications are hereby incorporated by reference intheir entirety.

FIELD OF THE INVENTION

The present invention relates to Alzheimer's Disease, amyloid proteinprecursor, amyloid beta peptide, and human aspartyl proteases, as wellas a method for the identification of agents that modulate the activityof these polypeptides and thereby are candidates to modulate theprogression of Alzheimer's disease.

BACKGROUND OF THE INVENTION

Alzheimer's disease (AD) causes progressive dementia with consequentformation of amyloid plaques, neurofibrillary tangles, gliosis andneuronal loss. The disease occurs in both genetic and sporadic formswhose clinical course and pathological features are quite similar. Threegenes have been discovered to date which, when mutated, cause anautosomal dominant form of Alzheimer's disease. These encode the amyloidprotein precursor (APP) and two related proteins, presenilin-1 (PS1) andpresenilin-2 (PS2), which, as their names suggest, are structurally andfunctionally related. Mutations in any of the three proteins have beenobserved to enhance proteolytic processing of APP via an intracellularpathway that produces amyloid beta peptide (Aβ peptide, or sometimeshere as Abeta), a 40-42 amino acid long peptide that is the primarycomponent of amyloid plaque in AD.

Dysregulation of intracellular pathways for proteolytic processing maybe central to the pathophysiology of AD. In the case of plaqueformation, mutations in APP, PS1 or PS2 consistently alter theproteolytic processing of APP so as to enhance formation of Aβ 1-42, aform of the Aβ peptide which seems to be particularly amyloidogenic, andthus very important in AD. Different forms of APP range in size from695-770 amino acids, localize to the cell surface, and have a singleC-terminal transmembrane domain. Examples of specific isotypes of APPwhich are currently known to exist in humans are the 695-amino acidpolypeptide described by Kang et. al. (1987), Nature 325: 733-736 whichis designated as the “normal” APP; the 751 amino acid polypeptidedescribed by Ponte et al. (1988), Nature 331: 525-527 (1988) and Tanziet al. (1988), Nature 331: 528-530; and the 770 amino acid polypeptidedescribed by Kitaguchi et. al. (1988), Nature 331: 530-532. The Abetapeptide is derived from a region of APP adjacent to and containing aportion of the transmembrane domain. Normally, processing of APP at theα-secretase site cleaves the midregion of the Aβ sequence adjacent tothe membrane and releases the soluble, extracellular domain of APP fromthe cell surface. This a-secretase APP processing creates soluble APP-α,which is normal and not thought to contribute to AD. Pathologicalprocessing of APP at the β- and γ-secretase sites, which are locatedN-terminal and C-terminal to the α-secretase site, respectively,produces a very different result than processing at the α site.Sequential processing at the β- and γ-secretase sites releases the Aβpeptide, a peptide possibly very important in AD pathogenesis.Processing at the β- and γ-secretase sites can occur in both theendoplasmic reticulum (in neurons) and in the endosomal/lysosomalpathway after reinternalization of cell surface APP (in all cells).Despite intense efforts, for 10 years or more, to identify the enzymesresponsible for processing APP at the β and γ sites, to produce the Aβpeptide, those proteases remained unknown until this disclosure.

SUMMARY OF THE INVENTION

Here, for the first time, we report the identification andcharacterization of the β secretase enzyme, termed Aspartyl Protease 2(Asp2). We disclose some known and some novel human aspartic proteasesthat can act as β-secretase proteases and, for the first time, weexplain the role these proteases have in AD. We describe regions in theproteases critical for their unique function and for the first timecharacterize their substrate. This is the first description of expressedisolated purified active protein of this type, assays that use theprotein, in addition to the identification and creation of useful celllines and inhibitors.

Here we disclose a number of variants of the Asp2 gene and peptide.

In one aspect, the invention provides any isolated or purified nucleicacid polynucleotide that codes for a protease capable of cleaving thebeta (β) secretase cleavage site of APP that contains two or more setsof special nucleic acids, where the special nucleic acids are separatedby nucleic acids that code for about 100 to 300 amino acid positions,where the amino acids in those positions may be any amino acids, wherethe first set of special nucleic acids consists of the nucleic acidsthat code for the peptide DTG, where the first nucleic acid of the firstspecial set of nucleic acids is the first special nucleic acid, andwhere the second set of nucleic acids code for either the peptide DSG orDTG, where the last nucleic acid of the second set of nucleic acids isthe last special nucleic acid, with the proviso that the nucleic acidsdisclosed in SEQ ID NO: 1 and SEQ ID NO: 3 are not included. In apreferred embodiment, the two sets of special nucleic acids areseparated by nucleic acids that code for about 125 to 222 amino acidpositions, which may be any amino acids. In a highly preferredembodiment, the two sets of special nucleic acids are separated bynucleic acids that code for about 150 to 196, or 150-190, or 150 to 172amino acid positions, which may be any amino acids. In a particularpreferred embodiment, the two sets are separated by nucleic acids thatcode for about 172 amino acid positions, which may be any amino acids.An exemplary nucleic acid polynucleotide comprises the acid nucleotidesequence in SEQ ID NO: 5. In another particular preferred embodiment,the two sets are separated by nucleic acids that code for about 196amino acids. An exemplary polynucleotide comprises the nucleotidesequence in SEQ ID NO: 5. In another particular embodiment, the two setsof nucleotides are separated by nucleic acids that code for about 190amino acids. An exemplary polynucleotide comprises the nucleotidesequence in SEQ ID NO: 1. Preferably, the first nucleic acid of thefirst special set of amino acids, that is, the first special nucleicacid, is operably linked to any codon where the nucleic acids of thatcodon codes for any peptide comprising from 1 to 10,000 amino acid(positions). In one variation, the first special nucleic acid isoperably linked to nucleic acid polymers that code for any peptideselected from the group consisting of: any reporter proteins or proteinswhich facilitate purification. For example, the first special nucleicacid is operably linked to nucleic acid polymers that code for anypeptide selected from the group consisting of: immunoglobin-heavy chain,maltose binding protein, glutathione S transferase, Green Fluorescentprotein, and ubiquitin. In another variation, the last nucleic acid ofthe second set of special amino acids, that is, the last special nucleicacid, is operably linked to nucleic acid polymers that code for anypeptide comprising any amino acids from 1 to 10,000 amino acids. Instill another variation, the last special nucleic acid is operablylinked to nucleic acid polymers that code for any peptide selected fromthe group consisting of: any reporter proteins or proteins whichfacilitate purification. For example, the last special nucleic acid isoperably linked to nucleic acid polymers that code for any peptideselected from the group consisting of: immunoglobin-heavy chain, maltosebinding protein, glutathione S transferase, Green Fluorescent protein,and ubiquitin.

In a related aspect, the invention provides any isolated or purifiednucleic acid polynucleotide that codes for a protease capable ofcleaving the beta secretase cleavage site of APP that contains two ormore sets of special nucleic acids, where the special nucleic acids areseparated by nucleic acids that code for about 100 to 300 amino acidpositions, where the amino acids in those positions may be any aminoacids, where the first set of special nucleic acids consists of thenucleic acids that code for DTG, where the first nucleic acid of thefirst special set of nucleic acids is the first special nucleic acid,and where the second set of nucleic acids code for either DSG or DTG,where the last nucleic acid of the second set of special nucleic acidsis the last special nucleic acid, where the first special nucleic acidis operably linked to nucleic acids that code for any number of aminoacids from zero to 81 amino acids and where each of those codons maycode for any amino acid. In a preferred embodiment, the first specialnucleic acid is operably linked to nucleic acids that code for anynumber of from 64 to 77 amino acids where each codon may code for anyamino acid. In a particular embodiment, the first special nucleic acidis operably linked to nucleic acids that code for 71 amino acids. Forexample, the first special nucleic acid is operably linked to 71 aminoacids and where the first of those 71 amino acids is the amino acid T.In a preferred embodiment, the polynucleotide comprises a sequence thatis at least 95% identical to a human Asp1 or Asp2 sequence as taughtherein. In another preferred embodiment, the first special nucleic acidis operably linked to nucleic acids that code for any number of from 30to 54 amino acids, or 35 to 47 amino acids, or 40 to 54 amino acidswhere each codon may code for any amino acid. In a particularembodiment, the first special nucleic acid is operably linked to nucleicacids that code for 47 amino acids. For example, the first specialnucleic acid is operably linked to 47 codons where the first those 47amino acids is the amino acid E.

In another related aspect, the invention provides for any isolated orpurified nucleic acid polynucleotide that codes for a protease capableof cleaving the beta (β) secretase cleavage site of APP and thatcontains two or more sets of special nucleic acids, where the specialnucleic acids are separated by nucleic acids that code for about 100 to300 amino acid positions, where the amino acids in those positions maybe any amino acids, where the first set of special nucleic acidsconsists of the nucleic acids that code for the peptide DTG, where thefirst nucleic acid of the first special set of amino acids is, the firstspecial nucleic acid, and where the second set of special nucleic acidscode for either the peptide DSG or DTG, where the last nucleic acid ofthe second set of special nucleic acids, the last special nucleic acid,is operably linked to nucleic acids that code for any number of codonsfrom 50 to 170 codons. In a preferred embodiment, the last specialnucleic acid is operably linked to nucleic acids comprising from 100 to170 codons. In a highly preferred embodiment, the last special nucleicacid is operably linked to nucleic acids comprising from 142 to 163codons. In a particular embodiment, the last special nucleic acid isoperably linked to nucleic acids comprising about 142 codons, or about163 codons, or about 170 codons. In a highly preferred embodiment, thepolynucleotide comprises a sequence that is at least 95% identical toaspartyl-protease encoding sequences taught herein. In one variation,the second set of special nucleic acids code for the peptide DSG. Inanother variation, the first set of nucleic acid polynucleotide isoperably linked to a peptide purification tag. For example, the nucleicacid polynucleotide is operably linked to a peptide purification tagwhich is six histidine. In still another variation, the first set ofspecial nucleic acids are on one polynucleotide and the second set ofspecial nucleic acids are on a second polynucleotide, where both firstand second polynucleotides have at lease 50 codons. In one embodiment ofthis type, both of the polynucleotides are in the same solution. In arelated aspect, the invention provides a vector which contains apolynucleotide as described above, or a cell or cell line which istransformed or transfected with a polynucleotide as described above orwith a vector containing such a polynucleotide.

In still another aspect, the invention provides an isolated or purifiedpeptide or protein comprising an amino acid polymer that is a proteasecapable of cleaving the beta (β) secretase cleavage site of APP thatcontains two or more sets of special amino acids, where the specialamino acids are separated by about 100 to 300 amino acid positions,where each amino acid position can be any amino acid, where the firstset of special amino acids consists of the peptide DTG, where the firstamino acid of the first special set of amino acids is, the first specialamino acid, where the second set of amino acids is selected from thepeptide comprising either DSG or DTG, where the last amino acid of thesecond set of special amino acids is the last special amino acid, withthe proviso that the proteases disclosed in SEQ ID NO: 2 and SEQ ID NO:4 are not included. In preferred embodiments, the two sets of aminoacids are separated by about 125 to 222 amino acid positions or about150 to 196 amino acids, or about 150-190 amino acids, or about 150 to172 amino acids, where in each position it may be any amino acid. In aparticular embodiment, the two sets of amino acids are separated byabout 172 amino acids. For example, the protease has the amino acidsequence described in SEQ ID NO 6. In another particular embodiment, thetwo sets of amino acids are separated by about 196 amino acids. Forexample, the two sets of amino acids are separated by the same aminoacid sequences that separate the same set of special amino acids in SEQID NO 4. In another particular embodiment, the two sets of nucleotidesare separated by about 190 amino acids. For example, the two sets ofnucleotides are separated by the same amino acid sequences that separatethe same set of special amino acids in SEQ ID NO 2. In one embodiment,the first amino acid of the first special set of amino acids, that is,the first special amino acid, is operably linked to any peptidecomprising from 1 to 10,000 amino acids. In another embodiment, thefirst special amino acid is operably linked to any peptide selected fromthe group consisting of: any reporter proteins or proteins whichfacilitate purification. In particular embodiments, the first specialamino acid is operably linked to any peptide selected from the groupconsisting of: immunoglobin-heavy chain, maltose binding protein,glutathione S transferase, Green Fluorescent protein, and ubiquitin. Instill another variation, the last amino acid of the second set ofspecial amino acids, that is, the last special amino acid, is operablylinked to any peptide comprising any amino acids from 1 to 10,000 aminoacids. By way of nonlimiting example, the last special amino acid isoperably linked any peptide selected from the group consisting of anyreporter proteins or proteins which facilitate purification. Inparticular embodiments, the last special amino acid is operably linkedto any peptide selected from the group consisting of: immunoglobin-heavychain, maltose binding protein, glutathione S transferase, GreenFluorescent protein, and ubiquitin.

In a related aspect, the invention provides any isolated or purifiedpeptide or protein comprising an amino acid polypeptide that codes for aprotease capable of cleaving the beta secretase cleavage site of APPthat contains two or more sets of special amino acids, where the specialamino acids are separated by about 100 to 300 amino acid positions,where each amino acid in each position can be any amino acid, where thefirst set of special amino acids consists of the amino acids DTG, wherethe first amino acid of the first special set of amino acids is, thefirst special amino acid, D, and where the second set of amino acids iseither DSG or DTG, where the last amino acid of the second set ofspecial amino acids is the last special amino acid, G, where the firstspecial amino acid is operably linked to amino acids that code for anynumber of amino acids from zero to 81 amino acid positions where in eachposition it may be any amino acid. In a preferred embodiment, the firstspecial amino acid is operably linked to a peptide from about 30-77 orabout 64 to 77 amino acids positions where each amino acid position maybe any amino acid. In a particular embodiment, the first special aminoacid is operably linked to a peptide 35, 47, 71, or 77 amino acids. In avery particular embodiment, the first special amino acid is operablylinked to 71 amino acids and the first of those 71 amino acids is theamino acid T. For example, the polypeptide comprises a sequence that isat least 95% identical to an aspartyl protease sequence as describedherein. In another embodiment, the first special amino acid is operablylinked to any number of from 40 to 54 amino acids (positions) where eachamino acid position may be any amino acid. In a particular embodiment,the first special amino acid is operably linked to amino acids that codefor a peptide of 47 amino acids. In a very particular embodiment, thefirst special amino acid is operably linked to a 47 amino acid peptidewhere the first those 47 amino acids is the amino acid E. In anotherparticular embodiment, the first special amino acid is operably linkedto the same corresponding peptides from SEQ ID NO. 4 that are 35, 47,71, or 77 peptides in length, beginning counting with the amino acids onthe first special sequence, DTG, towards the N-terminal of SEQ ID NO. 4.In another particular embodiment, the polypeptide comprises a sequencethat is at least 95% identical to the same corresponding amino acids inSEQ ID NO. 4, that is, identical to that portion of the sequences in SEQID NO. 4, including all the sequences from both the first and or thesecond special nucleic acids, toward the terminal, through and including71, 47, 35 amino acids before the first special amino acids. Forexample, the complete polypeptide comprises the peptide of 71 aminoacids, where the first of the amino acid is T and the second is Q.

In still another related aspect, the invention provides any isolated orpurified amino acid polypeptide that is a protease capable of cleavingthe beta (β) secretase cleavage site of APP that contains two or moresets of special amino acids, where the special amino acids are separatedby about 100 to 300 amino acid positions, where each amino acid in eachposition can be any amino acid, where the first set of special aminoacids consists of the amino acids that code for DTG, where the firstamino acid of the first special set of amino acids is, the first specialamino acid, D, and where the second set of amino acids are either DSG orDTG, where the last amino acid of the second set of special amino acidsis the last special amino acid, G, which is operably linked to anynumber of amino acids from 50 to 170 amino acids, which may be any aminoacids. In preferred embodiments, the last special amino acid is operablylinked to a peptide of about 100 to 170 amino acids or about 142-163amino acids. In particular embodiments, the last special amino acid isoperably linked to a peptide of about 142 amino acids, or about 163amino acids, or about 170 amino acids. For example, the polypeptidecomprises a sequence that is at least 95% identical (and preferably 100%identical) to an aspartyl protease sequence as described herein. In oneparticular embodiment, the second set of special amino acids iscomprised of the peptide with the amino acid sequence DSG. Optionally,the amino acid polypeptide is operably linked to a peptide purificationtag, such as purification tag which is six histidine. In one variation,the first set of special amino acids are on one polypeptide and thesecond set of special amino acids are on a second polypeptide, whereboth first and second polypeptide have at lease 50 amino acids, whichmay be any amino acids. In one embodiment of this type, both of thepolypeptides are in the same vessel. The invention further includes aprocess of making any of the polynucleotides, vectors, or cellsdescribed herein; and a process of making any of the polypeptidesdescribed herein.

In yet another related aspect, the invention provides a purifiedpolynucleotide comprising a nucleotide sequence that encodes apolypeptide having aspartyl protease activity, wherein the polypeptidehas an amino acid sequence characterized by: (a) a first tripeptidesequence DTG; (b) a second tripeptide sequence selected from the groupconsisting of DSG and DTG; and (c) about 100 to 300 amino acidsseparating the first and second tripeptide sequences, wherein thepolypeptide cleaves the beta secretase cleavage site of amyloid proteinprecursor. In one embodiment, the polypeptide comprises an amino acidsequence depicted in SEQ ID NO: 2 or 4, whereas in another embodiment,the polypeptide comprises an amino acid sequence other than the aminoacid sequences set forth in SEQ ID NOS: 2 and 4. Similarly, theinvention provides a purified polynucleotide comprising a nucleotidesequence that encodes a polypeptide that cleaves the beta secretasecleavage site of amyloid protein precursor; wherein the polynucleotideincludes a strand that hybridizes to one or more of SEQ ID NOS: 3, 5,and 7 under the following hybridization conditions: hybridizationovernight at 42° C. for 2.5 hours in 6×SSC/0.1% SDS, followed by washingin 1.0×SSC at 65° C., 0.1% SDS. In one embodiment, the polypeptidecomprises an amino acid sequence depicted in SEQ ID NO: 2 or 4, whereasin another embodiment, the polypeptide comprises an amino acid sequenceother than the amino acid sequences set forth in SEQ ID NOS: 2 and 4.Likewise, the invention provides a purified polypeptide having aspartylprotease activity, wherein the polypeptide is encoded by polynucleotidesas described in the preceding sentences. The invention also provides avector or host cell comprising such polynucleotides, and a method ofmaking the polypeptides using the vectors or host cells to recombinantlyexpress the polypeptide.

In yet another aspect, the invention provides an isolated nucleic acidmolecule comprising a polynucleotide, said polynucleotide encoding aHu-Asp polypeptide and having a nucleotide sequence at least 95%identical to a sequence selected from the group consisting of:

(a) a nucleotide sequence encoding a Hu-Asp polypeptide selected fromthe group consisting of Hu-Asp1, Hu-Asp2(a), and Hu-Asp2(b), whereinsaid Hu-Asp1, Hu-Asp2(a) and Hu-Asp2(b) polypeptides have the completeamino acid sequence of SEQ ID NO: 2, SEQ ID NO: 4, and SEQ ID NO: 6,respectively; and

(b) a nucleotide sequence complementary to the nucleotide sequence of(a).

Several species are particularly contemplated. For example, theinvention provides a nucleic acid molecule wherein said Hu-Asppolypeptide is Hu-Asp1, and said polynucleotide molecule of (a)comprises the nucleotide sequence of SEQ ID NO: 1; and a nucleic acidmolecule wherein said Hu-Asp polypeptide is Hu-Asp2(a), and saidpolynucleotide molecule of (a) comprises the nucleotide sequence of SEQID NO: 3; and a nucleic acid molecule wherein said Hu-Asp polypeptide isHu-Asp2(b), and said polynucleotide molecule of (a) comprises thenucleotide sequence of SEQ ID NO: 5. In addition to the foregoing, theinvention provides an isolated nucleic acid molecule comprising apolynucleotide which hybridizes under stringent conditions to apolynucleotide having the nucleotide sequence in (a) or (b) as describedabove.

Additionally, the invention provides a vector comprising a nucleic acidmolecule as described in the preceding paragraph. In a preferredembodiment, the nucleic acid molecule is operably linked to a promoterfor the expression of a Hu-Asp polypeptide. Individual vectors whichencode Hu-Asp1, and Hu-Asp2(a), and Hu-Asp2(b) are all contemplated.Likewise, the invention contemplates a host cell comprising any of theforegoing vectors, as well as a method of obtaining a Hu-Asp polypeptidecomprising culturing such a host cell and isolating the Hu-Asppolypeptide. Host cells of the invention include bacterial cells, suchas E. coli, and eukaryotic cells. Among the eukaryotic cells that arecontemplated are insect cells, such as sf9 or High 5 cells; andmammalian cells, such as human, rodent, lagomorph, and primate.Preferred human cells include HEK293, and IMR-32 cells. Other preferredmammalian cells include COS-7, CHO-K1, Neuro-2A, and 3T3 cells. Alsoamong the eukaryotic cells that are contemplated are a yeast cell and anavian cell.

In a related aspect, the invention provides an isolated Hu-Asp1polypeptide comprising an amino acid sequence at least 95% identical toa sequence comprising the amino acid sequence of SEQ ID NO: 2. Theinvention also provides an isolated Hu-Asp2(a) polypeptide comprising anamino acid sequence at least 95% identical to a sequence comprising theamino acid sequence of SEQ ID NO: 4. The invention also provides anisolated Hu-Asp2(a) polypeptide comprising an amino acid sequence atleast 95% identical to a sequence comprising the amino acid sequence ofSEQ ID NO: 8.

In still another aspect, the invention provides an isolated antibodythat binds specifically to any Hu-Asp polypeptide described herein,especially the polypeptide described in the preceding paragraphs.

The invention also provides several assays involving aspartyl proteaseenzymes of the invention. For example, the invention provides

a method to identify a cell that can be used to screen for inhibitors ofβ secretase activity comprising:

(a) identifying a cell that expresses a protease capable of cleaving APPat the β secretase site, comprising:

i) collect the cells or the supernatant from the cells to be identified

ii) measure the production of a critical peptide, where the criticalpeptide is selected from the group consisting of either the APPC-terminal peptide or soluble APP,

iii) select the cells which produce the critical peptide.

In one variation, the cells are collected and the critical peptide isthe APP C-terminal peptide created as a result of the β secretasecleavage. In another variation, the supernatant is collected and thecritical peptide is soluble APP, where the soluble APP has a C-terminuscreated by β secretase cleavage. In preferred embodiments, the cellscontain any of the nucleic acids or polypeptides described above and thecells are shown to cleave the β secretase site of any peptide having thefollowing peptide structure, P2, P1, P1′, P2′ (SEQ ID NO: 74), where P2is K or N, where P1 is M or L, where P1′ is D, where P2′ is A. In oneembodiment P2 is K and P1 is M and in another embodiment P2 is N and P1is L.

In still another aspect, the invention provides novel isoforms ofamyloid protein precursor (APP) where the last two carboxy terminusamino acids of that isoform are both lysine residues. In this context,the term “isoform” is defined as any APP polypeptide, including APPvariants (including mutations), and APP fragments that exists in humans,such as those described in U.S. Pat. No. 5,766,846, col 7, lines 45-67,incorporated into this document by reference, modified as describedherein by the inclusion of two C-terminal lysine residues. For example,the invention provides a polypeptide comprising the isoform known asAPP695, modified to include two lysine residues as its last two carboxyterminus amino acids. An exemplary polypeptide comprises the amino acidsequence set forth in SEQ ID NO: 16. The invention further includes APPisoform variants as set forth in SEQ ID NOS: 18 and 20. The inventionfurther includes all polynucleotides that encode an APP protein that hasbeen modified to include two C-terminal lysines; as well has anyeukaryotic cell line comprising such nucleic acids or polypeptides.Preferred cell lines include a mammalian cell line (e.g., HEK293,Neuro2a).

Thus, in one embodiment, the invention provides a polypeptide comprisingthe amino acid sequence of a mammalian amyloid protein precursor (APP)or fragment thereof containing an APP cleavage site recognizable by amammalian β-secretase, and further comprising two lysine residues at thecarboxyl terminus of the amino acid sequence of the mammalian APP or APPfragment. As taught herein in detail, the addition of two additionallysine residues to APP sequences has been found to greatly increase Aβprocessing of the APP in APP processing assays. Thus, the di-lysinemodified APP reagents of the invention are particularly useful in assaysto identify modulators of Aβ production, for use in designingtherapeutics for the treatment or prevention of Alzheimer's disease. Inone embodiment, the polypeptide comprises the complete amino acidsequence of a mammalian amyloid protein precursor (APP), and furthercomprises the two lysine residues at the carboxyl terminus of the aminoacid sequence of the mammalian amyloid protein precursor. In analternative embodiment, the polypeptide comprises only a fragment of theAPP, the fragment containing at least that portion of APP that iscleaved by a mammalian β-secretase in the formation of Aβ peptides.

The practice of assays that monitor cleavage of APP can be facilitatedby attaching a marker to a portion of the APP. Measurment of retained orliberated marker can be used to quantitate the amount of APP cleavagethat occurs in the assay, e.g., in the presence or absence of a putativemodulator of cleavage activity. Thus, in one preferred embodiment, thepolypeptide of the invention further includes a marker. For example, themarker comprises a reporter protein amino acid sequence attached to theAPP amino acid sequence. Exemplary reporter proteins include afluorescing protein (e.g., green fluorescing proteins, luciferase) or anenzyme that is used to cleave a substrate to produce a colorimetriccleavage product. Also contemplated are tag sequences which are commonlyused as epitopes for quantitative immunoassays.

In a preferred embodiment, the di-lysine-modified APP of the inventionis a human APP. For example, human APP isoforms such as APP695, APP751,and APP770, modified to include the two lysines, are contemplated. In apreferred embodiment, the APP isoform comprises at least one variationselected from the group consisting of a Swedish KM→NL mutation and aLondon V717→F mutation, or any other mutation that has been observed ina subpopulation that is particularly prone to development of Alzheimer'sdisease. These mutations are recognized as mutations that influence APPprocessing into Aβ. In a highly preferred embodiment, the APP protein orfragment thereof comprises the APP-Sw β-secretase peptide sequence NLDA(SEQ ID NO: 66), which is associated with increased levels of Aβprocessing and therefore is particularly useful in assays relating toAlzheimer's research. More particularly, the APP protein or fragmentthereof preferably comprises the APP-Sw β-secretase peptide sequenceSEVNLDAEFR (SEQ ID NO: 63).

In one preferred embodiment, the APP protein or fragment thereof furtherincludes an APP transmembrane domain carboxy-terminal to the APP-Swβ-secretase peptide sequence. Polypeptides that include the TM domainare particularly useful in cell-based APP processing assays. Incontrast, embodiments lacking the TM domain are useful in cell-freeassays of APP processing.

In addition to working with APP from humans and various animal models,researchers in the field of Alzheimer's also have construct chimeric APPpolypeptides which include stretches of amino acids from APP of onespecies (e.g., humans) fused to streches of APP from one or more otherspecies (e.g., rodent). Thus, in another embodiment of the polypeptideof the invention, the APP protein or fragment thereof comprises achimeric APP, the chimeric APP including partial APP amino acidsequences from at least two species. A chimeric APP that includes aminoacid sequence of a human APP and a rodent APP is particularlycontemplated.

In a related aspect, the invention provides a polynucleotide comprisinga nucleotide sequence that encodes a polypeptide as described in thepreceding paragraphs. Such a polynucleotide is useful for recombinantexpression of the polypeptide of the invention for use in APP processingassays. In addition, the polynucleotide is useful for transforming intocells to produce recombinant cells that express the polypeptide of theinvention, which cells are useful in cell-based assays to identifymodulators of APP processing. Thus, in addition to polynucleotides, theinvention provides a vector comprising such polynucleotides, especiallyexpression vectors where the polynucleotide is operably linked to apromoter to promote expression of the polypeptide encoded by thepolynucleotide in a host cell. The invention further provides a hostcell transformed or transfected with a polynucleotide of the inventionor a vector of the invention. Among the preferred host cells aremammalian cells, especially human cells.

In another, related embodiment, the invention provides a polypeptideuseful for assaying for modulators of β-secretase activity, saidpolypeptide comprising an amino acid sequence of the formulaNH₂—X—Y-Z-KK—COOH; wherein X, Y, and Z each comprise an amino acidsequence of at least one amino acid; wherein —NH₂—X comprises anamino-terminal amino acid sequence having at least one amino acidresidue; wherein Y comprises an amino acid sequence of a β-secretaserecognition site of a mammalian amyloid protein precursor (APP); andwherein Z-KK—COOH comprises a carboxy-terminal amino acid sequenceending in two lysine (K) residues. In one preferred variation, thecarboxyl-terminal amino acid sequence Z includes a hyrdrophobic domainthat is a transmembrane domain in host cells that express thepolypeptide. Host cells that express such a polypeptide are particularlyuseful in assays described herein for identifying modulators of APPprocessing. In another preferred variation, the amino-terminal aminoacid sequence X includes an amino acid sequence of a reporter or markerprotein, as described above. In still another preferred variation, theβ-secretase recognition site Y comprises the human APP-Sw β-secretasepeptide sequence NLDA (SEQ ID NO: 66). It will be apparent that thesepreferred variations are not mutually exclusive of each other—they maybe combined in a single polypeptide. The invention further provides apolynucleotide comprising a nucleotide sequence that encodes suchpolypeptides, vectors which comprise such polynucleotides, and hostcells which comprises such vectors, polynucleotides, and/orpolypeptides.

In yet another aspect, the invention provides a method for identifyinginhibitors of an enzyme that cleaves the beta secretase cleavable siteof APP comprising:

a) culturing cells in a culture medium under conditions in which theenzyme causes processing of APP and release of amyloid beta-peptide intothe medium and causes the accumulation of CTF99 fragments of APP in celllysates,

b) exposing the cultured cells to a test compound; and specificallydetermining whether the test compound inhibits the function of theenzyme by measuring the amount of amyloid beta-peptide released into themedium and/or the amount of CTF99 fragments of APP in cell lysates;

c) identifying test compounds diminishing the amount of soluble amyloidbeta peptide present in the culture medium and diminution of CTF99fragments of APP in cell lysates as Asp2 inhibitors. In preferredembodiments, the cultured cells are a human, rodent or insect cell line.It is also preferred that the human or rodent cell line exhibits βsecretase activity in which processing of APP occurs with release ofamyloid beta-peptide into the culture medium and accumulation of CTF99in cell lysates. Among the contemplated test compounds are antisenseoligomers directed against the enzyme that exhibits β secretaseactivity, which oligomers reduce release of soluble amyloid beta-peptideinto the culture medium and accumulation of CTF99 in cell lysates.

In yet another aspect, the invention provides a method for theidentification of an agent that decreases the activity of a Hu-Asppolypeptide selected from the group consisting of Hu-Asp1, Hu-Asp2(a),and Hu-Asp2(b), the method comprising:

a) determining the activity of said Hu-Asp polypeptide in the presenceof a test agent and in the absence of a test agent; and

b) comparing the activity of said Hu-Asp polypeptide determined in thepresence of said test agent to the activity of said Hu-Asp polypeptidedetermined in the absence of said test agent; whereby a lower level ofactivity in the presence of said test agent than in the absence of saidtest agent indicates that said test agent has decreased the activity ofsaid Hu-Asp polypeptide.

In a related aspect, the invention provides a method for assaying formodulators of β-secretase activity, comprising the steps of:

(a) contacting a first composition with a second composition both in thepresence and in the absence of a putative modulator compound, whereinthe first composition comprises a mammalian β-secretase polypeptide orbiologically active fragment thereof, and wherein the second compositioncomprises a substrate polypeptide having an amino acid sequencecomprising a β-secretase cleavage site; (b) measuring cleavage of thesubstrate polypeptide in the presence and in the absence of the putativemodulator compound; and (c) identifying modulators of β-secretaseactivity from a difference in cleavage in the presence versus in theabsence of the putative modulator compound. A modulator that is aβ-secretase antagonist (inhibitor) reduces such cleavage, whereas amodulator that is a β-secretase agonist increases such cleavage. Sincesuch assays are relevant to development of Alzheimer's diseasetherapeutics for humans, it will be readily apparent that, in onepreferred embodiment, the first composition comprises a purified humanAsp2 polypeptide. In one variation, the first composition comprises asoluble fragment of a human Asp2 polypeptide that retains Asp2β-secretase activity. Several such fragments (including ΔTM fragments)are described herein in detail. Thus, in a particular embodiment, thesoluble fragment is a fragment lacking an Asp2 transmembrane domain.

The β-secretase cleavage site in APP is known, and it will beappreciated that the assays of the invention can be performed witheither-intact APP or fragments or analogs of APP that retain theβ-secretase recognition and cleavage site. Thus, in one variation, thesubstrate polypeptide of the second composition comprises the amino acidsequence SEVNLDAEFR (SEQ ID NO: 63), which includes the β-secretaserecognition site of human APP that contains the “Swedish” mutation. Inanother variation, the substrate polypeptide of the second compositioncomprises the amino acid sequence EVKMDAEF (SEQ ID NO: 67). In anothervariation, the second composition comprises a polypeptide having anamino acid sequence of a human amyloid precursor protein (APP). Forexample, the human amyloid precursor protein is selected from the groupconsisting of: APP695, APP751, and APP770. Preferably, the human amyloidprecursor protein (irrespective of isoform selected) includes at leaston mutation selected from a KM→NL Swedish mutation and a V→F Londonmutation. As explained elsewhere, one preferred embodiment involves avariation wherein the polypeptide having an amino acid sequence of ahuman APP further comprises an amino acid sequence comprising a markersequence attached amino-terminal to the amino acid sequence of the humanamyloid precursor protein. Preferably, the polypeptide having an aminoacid sequence of a human APP further comprises two lysine residuesattached to the carboxyl terminus of the amino acid sequence of thehuman APP. The assays can be performed in a cell free setting, usingcell-free enzyme and cell-free substrate, or can be performed in acell-based assaywherein the second composition comprises a eukaryoticcell that expresses amyloid precursor protein (APP) or a fragmentthereof containing a β-secretase cleavage site. Preferably, the APPexpressed by the host cell is an APP variant that includes twocarboxyl-terminal lysine residues. It will also be appreciated that theβ-secretase enzyme can be an enzyme that is expressed on the surface ofthe same cells.

The present invention provides isolated nucleic acid moleculescomprising a polynucleotide that codes for a polypeptide selected fromthe group consisting of human aspartyl proteases. In particular, humanaspartyl protease 1 (Hu-Asp1) and two alternative splice variants ofhuman aspartyl protease-2 (Hu-Asp2), a “long” (L) form designated hereinas Hu-Asp2(a) and a “short” (S) form designated Hu-Asp2(b). As usedherein, all references to “Hu-Asp” should be understood to refer to allof Hu-Asp1, Hu-Asp2(a), and Hu-Asp2(b). In addition, as used herein, allreferences to “Hu-Asp2” should be understood to refer to both Hu-Asp2(a)and Hu-Asp2(b). Hu-Asp1 is expressed most abundantly in pancreas andprostate tissues, while Hu-Asp2(a) and Hu-Asp2(b) are expressed mostabundantly in pancreas and brain tissues. The invention also providesisolated Hu-Asp1, Hu-Asp2(a), and Hu-Asp2(b) polypeptides, as well asfragments thereof which exhibit aspartyl protease activity.

In a preferred embodiment, the nucleic acid molecules comprise apolynucleotide having a nucleotide sequence selected from the groupconsisting of residues 1-1554 of SEQ ID NO: 1, encoding Hu-Asp1,residues 1-1503 of SEQ ID NO: 3, encoding Hu-Asp2(a), and residues1-1428 of SEQ ID NO: 5, encoding Hu-Asp2(b). In another aspect, theinvention provides an isolated nucleic acid molecule comprising apolynucleotide which hybridizes under stringent conditions to apolynucleotide encoding Hu-Asp1, Hu-Asp2(a), Hu-Asp-2(b), or fragmentsthereof.

European patent application EP 0 848 062 discloses a polypeptidereferred to as “Asp 1,” that bears substantial homology to Hu-Asp1,while international application WO 98/22597 discloses a polypeptidereferred to as “Asp 2,” that bears substantial homology to Hu-Asp2(a).

The present invention also provides vectors comprising the isolatednucleic acid molecules of the invention, host cells into which suchvectors have been introduced, and recombinant methods of obtaining aHu-Asp1, Hu-Asp2(a), or Hu-Asp2(b) polypeptide comprising culturing theabove-described host cell and isolating the relevant polypeptide.

In another aspect, the invention provides isolated Hu-Asp1, Hu-Asp2(a),and Hu-Asp2(b) polypeptides, as well as fragments thereof. In apreferred embodiment, the Hu-Asp1, Hu-Asp2(a), and Hu-Asp2(b)polypeptides have the amino acid sequence given in SEQ ID NO: 2, SEQ IDNO: 4, or SEQ ID NO: 6, respectively. The present invention alsodescribes active forms of Hu-Asp2, methods for preparing such activeforms, methods for preparing soluble forms, methods for measuringHu-Asp2 activity, and substrates for Hu-Asp2 cleavage. The inventionalso describes antisense oligomers targeting the Hu-Asp1, Hu-Asp2(a) andHu-Asp2(b) mRNA transcripts and the use of such antisense reagents todecrease such mRNA and consequently the production of the correspondingpolypeptide. Isolated antibodies, both polyclonal and monoclonal, thatbinds specifically to any of the Hu-Asp1, Hu-Asp2(a), and Hu-Asp2(b)polypeptides of the invention are also provided.

The invention also provides a method for the identification of an agentthat modulates the activity of any of Hu-Asp-1, Hu-Asp2(a), andHu-Asp2(b). The inventions describes methods to test such agents incell-free assays to which Hu-Asp2 polypeptide is added, as well asmethods to test such agents in human or other mammalian cells in whichHu-Asp2 is present.

Additional features and variations of the invention will be apparent tothose skilled in the art from the entirety of this application,including the drawing and detailed description, and all such featuresare intended as aspects of the invention. Likewise, features of theinvention described herein can be re-combined into additionalembodiments that are also intended as aspects of the invention,irrespective of whether the combination of features is specificallymentioned above as an aspect or embodiment of the invention. Also, onlysuch limitations which are described herein as critical to the inventionshould be viewed as such; variations of the invention lackinglimitations which have not been described herein as critical areintended as aspects of the invention.

In addition to the foregoing, the invention includes, as an additionalaspect, all embodiments of the invention narrower in scope in any waythan the variations specifically mentioned above. Although theapplicant(s) invented the full scope of the claims appended hereto, theclaims appended hereto are not intended to encompass within their scopethe prior art work of others. Therefore, in the event that statutoryprior art within the scope of a claim is brought to the attention of theapplicants by a Patent Office or other entity or individual, theapplicant(s) reserve the right to exercise amendment rights underapplicable patent laws to redefine the subject matter of such a claim tospecifically exclude such statutory prior art or obvious variations ofstatutory prior art from the scope of such a claim. Variations of theinvention defined by such amended claims also are intended as aspects ofthe invention.

BRIEF DESCRIPTION OF THE SEQUENCE LISTING

Sequence ID NO: 1: Human Asp-1, nucleotide sequence.

Sequence ID NO: 2: Human Asp-1, predicted amino acid sequence.

Sequence ID NO: 3: Human Asp-2(a), nucleotide sequence.

Sequence ID NO: 4: Human Asp-2(a), predicted amino acid sequence. TheAsp2(a) amino acid sequence includes a putative signal peptidecomprising residues 1 to 21; and a putative pre-propeptide after thesignal peptide that extends through residue 45 (as assessed byprocessing observed of recombinant Asp2(a) in CHO cells), and a putativepropeptide that may extend to at least about residue 57, based on theobservation of an observed GRR↓GS (SEQ ID NO: 68) sequence which hascharacteristics of a protease recognition sequence. The Asp2(a) furtherincludes a transmembrane domain comprising residues 455-477, acytoplasmic domain comprising residues 478-501, and a putativealpha-helical spacer region, comprising residues 420-454, believed to beunnecessary for proteolytic activity, between the protease catalyticdomain and the transmembrane domain.

Sequence ID NO: 5: Human Asp-2(b), nucleotide sequence.

Sequence ID NO: 6: Human Asp-2(b), predicted amino acid sequence. TheAsp2(b) amino acid sequence includes a putative signal peptide,pre-propeptide, and propeptide as described above for Asp2(a). TheAsp2(b) further includes a transmembrane domain comprising residues430-452, a cytoplasmic domain comprising residues 453-476, and aputative alpha-helical spacer region, comprising residues 395-429,believed to be unnecessary for proteolytic activity, between theprotease catalytic domain and the transmembrane domain.

Sequence ID NO: 7: Murine Asp-2(a), nucleotide sequence.

Sequence ID NO: 8: Murine Asp-2(a), predicted amino acid sequence. Theproteolytic processing of murine Asp2(a) is believed to be analogous tothe processing described above for human Asp2(a). In addition, a variantlacking amino acid residues 190-214 of SEQ ID NO: 8 is specificallycontemplated as a murine Asp2(b) polypeptide.

Sequence ID NO: 9: Human APP695, nucleotide sequence.

Sequence ID NO: 10: Human APP695, predicted amino acid sequence.

Sequence ID NO: 11: Human APP695-Sw, nucleotide sequence.

Sequence ID NO: 12: Human APP695-Sw. predicted amino acid sequence. Inthe APP695 isoform, the Sw mutation is characterized by a KM→NLalteration at positions 595-596 (compared to normal APP695).

Sequence ID NO: 13: Human APP695-VF, nucleotide sequence.

Sequence ID NO: 14: Human APP695-VF, predicted amino acid sequence. Inthe APP 695 isoform, the VF mutation is characterized by a V→Falteration at position 642 (compared to normal APP 695).

Sequence ID NO: 15: Human APP695-KK, nucleotide sequence.

Sequence ID NO: 16: Human APP695-KK, predicted amino acid sequence.(APP695 with two carboxy-terminal lysine residues.)

Sequence ID NO: 17: Human APP695-Sw-KK, nucleotide sequence.

Sequence ID NO: 18: Human APP695-Sw-KK, predicted amino acid sequence.

Sequence ID NO: 19: Human APP695-VF-KK, nucleotide sequence.

Sequence ID NO: 20: Human APP695-VF-KK, predicted amino acid sequence.

Sequence ID NO: 21: T7-Human-pro-Asp-2(a)ΔTM, nucleotide sequence.

Sequence ID NO: 22: T7-Human-pro-Asp-2(a)ΔTM, amino acid sequence.

Sequence ID NO: 23: T7-Caspase-Human-pro-Asp-2(a)ΔTM, nucleotidesequence.

Sequence ID NO: 24: T7-Caspase-Human-pro-Asp-2(a)ΔTM, amino acidsequence.

Sequence ID NO: 25: Human-pro-Asp-2(a)ΔTM (low GC), nucleotide sequence.

Sequence ID NO: 26: Human-pro-Asp-2(a)ΔTM, (low GC), amino acidsequence.

Sequence ID NO: 27: T7-Caspase-Caspase 8 cleavage-Human-pro-Asp-2(a)ΔTM,nucleotide sequence.

Sequence ID NO: 28: T7-Caspase-Caspase 8 cleavage-Human-pro-Asp-2(a)ΔTM,amino acid sequence

Sequence ID NO: 29: Human Asp-2(a)ΔTM, nucleotide sequence.

Sequence ID NO: 30: Human Asp-2(a)ΔTM, amino acid sequence.

Sequence ID NO: 31: Human Asp-2(a)ΔTM(His)₆, nucleotide sequence.

Sequence ID NO: 32: Human Asp-2(a)ΔTM(His)₆, amino acid sequence.

Sequence ID NOS: 33-49 are short synthetic peptide and oligonucleotidesequences that are described below in the Detailed Description of theInvention.

Sequence ID NO: 50: Human Asp2(b)ΔTM polynucleotide sequence.

Sequence ID NO: 51: Human Asp2(b)ΔTM polypeptide sequence (exemplaryvariant of Human Asp2(b) lacking transmembrane and intracellular domainsof Hu-Asp2(b) set forth in SEQ ID NO: 6.

Sequence ID NO: 52: Human Asp2(b)ΔTM(His)₆ polynucleotide sequence.

Sequence ID NO: 53: Human Asp2(b)ΔTM(His)₆ polypeptide sequence (HumanAsp2(b)ΔTM with six histidine tag attached to C-terminus).

Sequence ID NO: 54: Human APP770-encoding polynucleotide sequence.

Sequence ID NO: 55: Human APP770 polypeptide sequence. To introduce theKM→NL Swedish mutation, residues KM at positions 670-71 are changed toNL. To introduce the V→F London mutation, the V residue at position 717is changed to F.

Sequence ID NO: 56: Human APP751 encoding polynucleotide sequence.

Sequence ID NO: 57: Human APP751 polypeptide sequence (Human APP751isoform).

Sequence ID NO: 58: Human APP770-KK encoding polynucleotide sequence.

Sequence ID NO: 59: Human APP770-KK polypeptide sequence. (Human APP770isoform to which two C-terminal lysines have been added).

Sequence ID NO: 60: Human APP751-KK encoding polynucleotide sequence.

Sequence ID NO: 61: Human APP751-KK polypeptide sequence (Human APP751isoform to which two C-terminal lysines have been added).

Sequence ID NOS: 62-65: Various short peptide sequences described indetail in detailed description.

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A-1B: FIGS. 1A-1B show the nucleotide (SEQ ID NO: 1) andpredicted amino acid sequence (SEQ ID NO: 2) of human Asp1.

FIGS. 2A-2B: FIGS. 2A-2B show the nucleotide (SEQ ID NO: 5) andpredicted amino acid sequence (SEQ ID NO: 6) of human Asp2(b).

FIGS. 3A-3B: FIGS. 3A-3B shows the nucleotide (SEQ ID NO: 3) andpredicted amino acid sequence (SEQ ID NO: 4) of human Asp2(a).

FIG. 4: FIG. 4 shows the nucleotide (SEQ ID NO: 7) and predicted aminoacid sequence (SEQ ID NO: 8) of murine Asp2(a).

FIG. 5: FIG. 5 shows the BestFit alignment of the predicted amino acidsequences of Hu-Asp2(a) (SEQ ID NO: 4) and murine Asp2(a) (SEQ ID NO:8).

FIGS. 6A-6B: FIGS. 6A-6B show the nucleotide (SEQ ID NO: 21) andpredicted amino acid sequence (SEQ ID NO: 22) ofT7-Human-pro-Asp-2(a)ΔTM.

FIGS. 7A-7B: FIGS. 7A-7B show the nucleotide (SEQ ID NO: 23) andpredicted amino acid sequence (SEQ ID NO: 24) ofT7-caspase-Human-pro-Asp-2(a)ΔTM.

FIGS. 8A-8B: FIGS. 8A-8B show the nucleotide (SEQ ID NO: 25) andpredicted amino acid sequence (SEQ ID NO: 26) of Human-pro-Asp-2(a)ΔTM(low GC).

FIG. 9: Western blot showing reduction of CTF99 production by HEK125.3cells transfected with antisense oligomers targeting the Hu-Asp2 mRNA.

FIG. 10: Western blot showing increase in CTF99 production in mouseNeuro-2a cells cotransfected with APP-KK with and without Hu-Asp2 onlyin those cells cotransfected with Hu-Asp2. A further increase in CTF99production is seen in cells cotransfected with APP-Sw-KK with andwithout Hu-Asp2 only in those cells cotransfected with Hu-Asp2.

FIG. 11: FIG. 11 shows the predicted amino acid sequence (SEQ ID NO: 30)of Human-Asp2(a)ΔTM.

FIG. 12: FIG. 12 shows the predicted amino acid sequence (SEQ ID NO: 30)of Human-Asp2(a)ΔTM(His)₆.

DETAILED DESCRIPTION OF THE INVENTION

A few definitions used in this invention follow, most definitions to beused are those that would be used by one ordinarily skilled in the art.

The term “β amyloid peptide” means any peptide resulting from betasecretase cleavage of APP. This includes peptides of 39, 40, 41, 42 and43 amino acids, extending from the β-secretase cleavage site to 39, 40,41, 42 and 43 amino acids C-terminal to the β-secretase cleavage site. βamyloid peptide also includes sequences 1-6, SEQ ID NOS: 1-6 of U.S.Pat. No. 5,750,349, issued May 12, 1998 (incorporated into this documentby reference). A β-secretase cleavage fragment disclosed here is calledCTF-99, which extends from β-secretase cleavage site to the carboxyterminus of APP.

When an isoform of APP is discussed then what is meant is any APPpolypeptide, including APP variants (including mutations), and APPfragments that exists in humans such as those described in U.S. Pat. No.5,766,846, col 7, lines 45-67, incorporated into this document byreference.

The term “β-amyloid precursor protein” (APP) as used herein is definedas a polypeptide that is encoded by a gene of the same name localized inhumans on the long arm of chromosome 21 and that includes “βAP—here“β-amyloid protein” see above, within its carboxyl third. APP is aglycosylated, single-membrane spanning protein expressed in a widevariety of cells in many mammalian tissues. Examples of specificisotypes of APP which are currently known to exist in humans are the 695amino acid polypeptide described by Kang et. al. (1987) Nature325:733-736 which is designated as the “normal” APP (SEQ ID NOS: 9-10);the 751 amino acid polypeptide described by Ponte et al. (1988) Nature331:525-527 (1988) and Tanzi et al. (1988) Nature 331:528-530 (SEQ IDNOS: 56-57); and the 770-amino acid polypeptide described by Kitaguchiet. al. (1988) Nature 331:530-532 (SEQ ID NOS: 54-55). Examples ofspecific variants of APP include point mutation which can differ in bothposition and phenotype (for review of known variant mutation see Hardy(1992) Nature Genet. 1:233-234). All references cited here incorporatedby reference. The term “APP fragments” as used herein refers tofragments of APP other than those which consist solely of βAP or βAPfragments. That is, APP fragments will include amino acid sequences ofAPP in addition to those which form intact βAP or a fragment of βAP.

When the term “any amino acid” is used, the amino acids referred to areto be selected from the following, three letter and single letterabbreviations—which may also be used, are provided as follows:

Alanine, Ala, A; Arginine, Arg, R; Asparagine, Asn, N; Aspartic acid,Asp, D; Cysteine, Cys, C; Glutamine, Gln, Q; Glutamic Acid, Glu, E;Glycine, Gly, G; Histidine, His, H; Isoleucine, Ile, I; Leucine, Leu, L;Lysine, Lys, K; Methionine, Met, M; Phenylalanine, Phe, F; Proline, Pro,P; Serine, Ser, S; Threonine, Thr, T; Tryptophan, Trp, W; Tyrosine, Tyr,Y; Valine, Val, V; Aspartic acid or Asparagine, Asx, B; Glutamic acid orGlutamine, Glx, Z; Any amino acid, Xaa, X.

The present invention describes a method to scan gene databases for thesimple active site motif characteristic of aspartyl proteases.Eukaryotic aspartyl proteases such as pepsin and renin possess atwo-domain structure which folds to bring two aspartyl residues intoproximity within the active site. These are embedded in the shorttripeptide motif DTG, or more rarely, DSG. Most aspartyl proteases occuras proenzyme whose N-terminus must be cleaved for activation. The DTG orDSG active site motif appears at about residue 65-70 in the proenzyme(prorenin, pepsinogen), but at about residue 25-30 in the active enzymeafter cleavage of the N-terminal prodomain. The limited length of theactive site motif makes it difficult to search collections of short,expressed sequence tags (EST) for novel aspartyl proteases. ESTsequences typically average 250 nucleotides or less, and so would encode80-90 amino acid residues or less. That would be too short a sequence tospan the two active site motifs. The preferred method is to scandatabases of hypothetical or assembled protein coding sequences. Thepresent invention describes a computer method to identify candidateaspartyl proteases in protein sequence databases. The method was used toidentify seven candidate aspartyl protease sequences in theCaenorhabditis elegans genome. These sequences were then used toidentify by homology search Hu-Asp1 and two alternative splice variantsof Hu-Asp2, designated herein as Hu-Asp2(a) and Hu-Asp2(b).

In a major aspect of the invention disclosed here we provide newinformation about APP processing. Pathogeneic processing of the amyloidprecursor protein (APP) via the Aβ pathway requires the sequentialaction of two proteases referred to as β-secretase and γ-secretase.Cleavage of APP by the β-secretase and γ-secretase generates theN-terminus and C-terminus of the Aβ peptide, respectively. Because overproduction of the Aβ peptide, particularly the Aβ₁₋₄₂, has beenimplicated in the initiation of Alzheimer's disease, inhibitors ofeither the β-secretase and/or the γ-secretase have potential in thetreatment of Alzheimer's disease. Despite the importance of theβ-secretase and γ-secretase in the pathogenic processing of APP,molecular definition of these enzymes has not been accomplished to date.That is, it was not known what enzymes were required for cleavage ateither the β-secretase or the γ-secretase cleavage site. The sitesthemselves were known because APP was known and the Aβ₁₋₄₂, peptide wasknown, see U.S. Pat. No. 5,766,846 and U.S. Pat. No. 5,837,672,(incorporated by reference, with the exception to reference to “soluble”peptides). But what enzyme was involved in producing the Aβ₁₋₄₂, peptidewas unknown.

Alignment of the amino acid sequences of Hu-Asp2 with other knownaspartyl proteases reveals a similar domain organization. All of thesequences contain a signal sequence followed by a pro-segment and thecatalytic domain containing 2 copies of the aspartyl protease activesite motif (DTG/DSG) separated by approximately 180 amino acid residues.Comparison of the processing site for proteolytic removal of thepro-segment in the mature forms of pepsin A, pepsin C, cathepsin D,cathepsin E and renin reveals that the mature forms of these enzymescontain between 31-35 amino acid residues upstream of the first DTGmotif. Inspection of this region in the Hu-Asp-2 amino acid sequenceindicates a preferred processing site within the sequence GRR↓GS (SEQ IDNO: 68) as proteolytic processing of pro-protein precursors commonlyoccurs at site following dibasic amino acid pairs (e.g. RR). Also,processing at this site would yield a mature enzyme with 35 amino acidresidues upstream of the first DTG, consistent with the processing sitesfor other aspartyl proteases. In the absence of self-activation ofHu-Asp2 or a knowledge of the endogenous protease that processes Hu-Asp2at this site, a recombinant form was engineered by introducing arecognition site for the PreSission protease (LEVLFQ↓GP; SEQ ID NO: 62)into the expression plasmids for bacterial, insect cell, and mammaliancell expression of pro-Hu-Asp2. In each case, the Gly residue in P1′position corresponds to the Gly residue 35 amino acids upstream of thefirst DTG motif in Hu-Asp2.

The present invention involves the molecular definition of several novelhuman aspartyl proteases and one of these, referred to as Hu-Asp-2(a)and Hu-Asp2(b), has been characterized in detail. Previous forms of asp1and asp 2 have been disclosed, see EP 0848062 A2 and EP 0855444A2,inventors David Powel et al., assigned to Smith Kline Beecham Corp.(incorporated by reference). Herein are disclosed old and new forms ofHu-Asp 2. For the first time they are expressed in active form, theirsubstrates are disclosed, and their specificity is disclosed. Prior tothis disclosure cell or cell extracts were required to cleave theβ-secretase site, now purified protein can be used in assays, alsodescribed here. Based on the results of (1) antisense knock outexperiments, (2) transient transfection knock in experiments, and (3)biochemical experiments using purified recombinant Hu-Asp-2, wedemonstrate that Hu-Asp-2 is the β-secretase involved in the processingof APP. Although the nucleotide and predicted amino acid sequence ofHu-Asp-2(a) has been reported, see above, see EP 0848062 A2 and EP0855444A2, no functional characterization of the enzyme was disclosed.Here the authors characterize the Hu-Asp-2 enzyme and are able toexplain why it is a critical and essential enzyme required in theformation of Aβ₁₋₄₂, peptide and possible a critical step in thedevelopment of AD.

In another embodiment the present invention also describes a novelsplice variant of Hu-Asp2, referred to as Hu-Asp-2(b), that has neverbefore been disclosed.

In another embodiment, the invention provides isolated nucleic acidmolecules comprising a polynucleotide encoding a polypeptide selectedfrom the group consisting of human aspartyl protease 1 (Hu-Asp1) and twoalternative splice variants of human aspartyl protease-2 (Hu-Asp2),designated herein as Hu-Asp2(a) and Hu-Asp2(b). As used herein, allreferences to “Hu-Asp2” should be understood to refer to both Hu-Asp2(a)and Hu-Asp2(b). Hu-Asp1 is expressed most abundantly in pancreas andprostate tissues, while Hu-Asp2(a) and Hu-Asp2(b) are expressed mostabundantly in pancreas and brain tissues. The invention also providesisolated Hu-Asp1, Hu-Asp2(a), and Hu-Asp2(b) polypeptides, as well asfragments thereof which exhibit aspartyl protease activity.

The predicted amino acid sequences of Hu-Asp1, Hu-Asp2(a) and Hu-Asp2(b)share significant homology with previously identified mammalian aspartylproteases such as pepsinogen A, pepsinogen B, cathepsin D, cathepsin E,and renin. P. B. Szecs, Scand. J. Clin. Lab. Invest. 52:(Suppl. 210 5-22(1992)). These enzymes are characterized by the presence of a duplicatedDTG/DSG sequence motif. The Hu-Asp1 and HuAsp2 polypeptides disclosedherein also exhibit extremely high homology with the ProSite consensusmotif for aspartyl proteases extracted from the SwissProt database.

The nucleotide sequence given as residues 1-1554 of SEQ ID NO: 1corresponds to the nucleotide sequence encoding Hu-Asp1, the nucleotidesequence given as residues 1-1503 of SEQ ID NO: 3 corresponds to thenucleotide sequence encoding Hu-Asp2(a), and the nucleotide sequencegiven as residues 1-1428 of SEQ ID NO: 5 corresponds to the nucleotidesequence encoding Hu-Asp2(b). The isolation and sequencing of DNAencoding Hu-Asp1, Hu-Asp2(a), and Hu-Asp2(b) is described below inExamples 1 and 2.

As is described in Examples 1 and 2, automated sequencing methods wereused to obtain the nucleotide sequence of Hu-Asp1, Hu-Asp2(a), andHu-Asp-2(b). The Hu-Asp nucleotide sequences of the present inventionwere obtained for both DNA strands, and are believed to be 100%accurate. However, as is known in the art, nucleotide sequence obtainedby such automated methods may contain some errors. Nucleotide sequencesdetermined by automation are typically at least about 90%, moretypically at least about 95% to at least about 99.9% identical to theactual nucleotide sequence of a given nucleic acid molecule. The actualsequence may be more precisely determined using manual sequencingmethods, which are well known in the art. An error in sequence whichresults in an insertion or deletion of one or more nucleotides mayresult in a frame shift in translation such that the predicted aminoacid sequence will differ from that which would be predicted from theactual nucleotide sequence of the nucleic acid molecule, starting at thepoint of the mutation. The Hu-Asp DNA of the present invention includescDNA, chemically synthesized DNA, DNA isolated by PCR, genomic DNA, andcombinations thereof. Genomic Hu-Asp DNA may be obtained by screening agenomic library with the Hu-Asp2 cDNA described herein, using methodsthat are well known in the art, or with oligonucleotides chosen from theHu-Asp2 sequence that will prime the polymerase chain reaction (PCR).RNA transcribed from Hu-Asp DNA is also encompassed by the presentinvention.

Due to the degeneracy of the genetic code, two DNA sequences may differand yet encode identical amino acid sequences. The present inventionthus provides isolated nucleic acid molecules having a polynucleotidesequence encoding any of the Hu-Asp polypeptides of the invention,wherein said polynucleotide sequence encodes a Hu-Asp polypeptide havingthe complete amino acid sequence of SEQ ID NO: 2, SEQ ID NO: 4, SEQ IDNO: 6, or fragments thereof.

Also provided herein are purified Hu-Asp polypeptides, both recombinantand non-recombinant. Most importantly, methods to produce Hu-Asp2polypeptides in active form are provided. These include production ofHu-Asp2 polypeptides and variants thereof in bacterial cells, insectcells, and mammalian cells, also in forms that allow secretion of theHu-Asp2 polypeptide from bacterial, insect or mammalian cells into theculture medium, also methods to produce variants of Hu-Asp2 polypeptideincorporating amino acid tags that facilitate subsequent purification.In a preferred embodiment of the invention the Hu-Asp2 polypeptide isconverted to a proteolytically active form either in transformed cellsor after purification and cleavage by a second protease in a cell-freesystem, such active forms of the Hu-Asp2 polypeptide beginning with theN-terminal sequence TQHGIR (SEQ ID NO: 69) or ETDEEP (SEQ ID NO: 70).The sequence TQHGIR (SEQ ID NO: 69) represents the amino-terminus ofAsp2(a) or Asp2(b) beginning with residue 22 of SEQ ID NO: 4 or 6, aftercleavage of a putative 21 residue signal peptide. Recombinant Asp2(a)expressed in and purified from insect cells was observed to have thisamino terminus, presumably as a result of cleavage by a signalpeptidase. The sequence ETDEEP (SEQ ID NO: 70) represents theamino-terminus of Asp2(a) or Asp2(b) beginning with residue 46 of SEQ IDNO: 4 or 6, as observed when Asp2(a) has been recombinantly produced inCHO cells (presumably after cleavage by both a rodent signal peptidaseand another rodent peptidase that removes a propeptide sequence). TheAsp2(a) produced in the CHO cells possesses β-secretase activity, asdescribed in greater detail in Examples 11 and 12. Variants andderivatives, including fragments, of Hu-Asp proteins having the nativeamino acid sequences given in SEQ ID NOS: 2, 4, and 6 that retain any ofthe biological activities of Hu-Asp are also within the scope of thepresent invention. Of course, one of ordinary skill in the art willreadily be able to determine whether a variant, derivative, or fragmentof a Hu-Asp protein displays Hu-Asp activity by subjecting the variant,derivative, or fragment to a standard aspartyl protease assay. Fragmentsof Hu-Asp within the scope of this invention include those that containthe active site domain containing the amino acid sequence DTG, fragmentsthat contain the active site domain amino acid sequence DSG, fragmentscontaining both the DTG and DSG active site sequences, fragments inwhich the spacing of the DTG and DSG active site sequences has beenlengthened, fragments in which the spacing has been shortened. Alsowithin the scope of the invention are fragments of Hu-Asp in which thetransmembrane domain has been removed to allow production of Hu-Asp2 ina soluble form. In another embodiment of the invention, the two halvesof Hu-Asp2, each containing a single active site DTG or DSG sequence canbe produced independently as recombinant polypeptides, then combined insolution where they reconstitute an active protease.

Thus, the invention provides a purified polypeptide comprising afragment of a mammalian Asp2 protein, wherein said fragment lacks theAsp2 transmembrane domain of said Asp2 protein, and wherein thepolypeptide and the fragment retain the β-secretase activity of saidmammalian Asp2 protein. In a preferred embodiment, the purifiedpolypeptide comprises a fragment of a human Asp2 protein that retainsthe β-secretase activity of the human Asp2 protein from which it wasderived. Examples include:

a purified polypeptide that comprises a fragment of Asp2(a) having theamino acid sequence set forth in SEQ ID NO: 4, wherein the polypeptidelacks transmembrane domain amino acids 455 to 477 of SEQ ID NO: 4;

a purified polypeptide as described in the preceding paragraph thatfurther lacks cytoplasmic domain amino acids 478 to 501 of SEQ ID NO: 4;

a purified polypeptide as described in either of the precedingparagraphs that further lacks amino acids 420-454 of SEQ ID NO: 4, whichconstitute a putative alpha helical region between the catalytic domainand the transmembrane domain that is believed to be unnecessary forβ-secretase activity;

a purified polypeptide that comprises an amino acid sequence thatincludes amino acids 58 to 419 of SEQ ID NO: 4, and that lacks aminoacids 22 to 57 of SEQ ID NO: 4;

a purified polypeptide that comprises an amino acid sequence thatincludes amino acids 46 to 419 of SEQ ID NO: 4, and that lacks aminoacids 22 to 45 of SEQ ID NO: 4;

a purified polypeptide that comprises an amino acid sequence thatincludes amino acids 22 to 454 of SEQ ID NO: 4.

a purified polypeptide that comprises a fragment of Asp2(b) having theamino acid sequence set forth in SEQ ID NO: 6, and wherein saidpolypeptide lacks transmembrane domain amino acids 430 to 452 of SEQ IDNO: 6;

a purified polypeptide as described in the preceding paragraph thatfurther lacks cytoplasmic domain amino acids 453 to 476 of SEQ ID NO: 6;

a purified polypeptide as described in either of the preceding twoparagraphs that further lacks amino acids 395-429 of SEQ ID NO: 6, whichconstitute a putative alpha helical region between the catalytic domainand the transmembrane domain that is believed to be unnecessary forβ-secretase activity;

a purified polypeptide comprising an amino acid sequence that includesamino acids 58 to 394 of SEQ ID NO: 6, and that lacks amino acids 22 to57 of SEQ ID NO: 6;

a purified polypeptide comprising an amino acid sequence that includesamino acids 46 to 394 of SEQ ID NO: 6, and that lacks amino acids 22 to45 of SEQ ID NO: 6; and

a purified polypeptide comprising an amino acid sequence that includesamino acids 22 to 429 of SEQ ID NO: 6.

Also included as part of the invention is a purified polynucleotidecomprising a nucleotide sequence that encodes such polypeptides; avector comprising a polynucleotide that encodes such polypeptides; and ahost cell transformed or transfected with such a polynucleotide orvector.

Hu-Asp variants may be obtained by mutation of native Hu-Asp-encodingnucleotide sequences, for example. A Hu-Asp variant, as referred toherein, is a polypeptide substantially homologous to a native Hu-Asppolypeptide but which has an amino acid sequence different from that ofnative Hu-Asp because of one or more deletions, insertions, orsubstitutions in the amino acid sequence. The variant amino acid ornucleotide sequence is preferably at least about 80% identical, morepreferably at least about 90% identical, and most preferably at leastabout 95% identical, to a native Hu-Asp sequence. Thus, a variantnucleotide sequence which contains, for example, 5 point mutations forevery one hundred nucleotides, as compared to a native Hu-Asp gene, willbe 95% identical to the native protein. The percentage of sequenceidentity, also termed homology, between a native and a variant Hu-Aspsequence may also be determined, for example, by comparing the twosequences using any of the computer programs commonly employed for thispurpose, such as the Gap program (Wisconsin Sequence Analysis Package,Version 8 for Unix, Genetics Computer Group, University Research Park,Madison Wis.), which uses the algorithm of Smith and Waterman (Adv.Appl. Math. 2. 482-489 (1981)).

Alterations of the native amino acid sequence may be accomplished by anyof a number of known techniques. For example, mutations may beintroduced at particular locations by procedures well known to theskilled artisan, such as oligonucleotide-directed mutagenesis, which isdescribed by Walder et al. (Gene 42:133 (1986)); Bauer et al. (Gene37:73 (1985)); Craik (BioTechniques, January 1985, pp. 12-19); Smith etal. (Genetic Engineering: Principles and Methods, Plenum Press (1981));and U.S. Pat. Nos. 4,518,584 and 4,737,462.

Hu-Asp variants within the scope of the invention may compriseconservatively substituted sequences, meaning that one or more aminoacid residues of a Hu-Asp polypeptide are replaced by different residuesthat do not alter the secondary and/or tertiary structure of the Hu-Asppolypeptide. Such substitutions may include the replacement of an aminoacid by a residue having similar physicochemical properties, such assubstituting one aliphatic residue (Ile, Val, Leu or Ala) for another,or substitution between basic residues Lys and Arg, acidic residues Gluand Asp, amide residues Gln and Asn, hydroxyl residues Ser and Thr, oraromatic residues Phe and Tyr. Further information regarding makingphenotypically silent amino acid exchanges may be found in Bowie et al.,Science 247:1306-1310 (1990). Other Hu-Asp variants which might retainsubstantially the biological activities of Hu-Asp are those where aminoacid substitutions have been made in areas outside functional regions ofthe protein.

In another aspect, the invention provides an isolated nucleic acidmolecule comprising a polynucleotide which hybridizes under stringentconditions to a portion of the nucleic acid molecules described above,e.g., to at least about 15 nucleotides, preferably to at least about 20nucleotides, more preferably to at least about 30 nucleotides, and stillmore preferably to at least about from 30 to at least about 100nucleotides, of one of the previously described nucleic acid molecules.Such portions of nucleic acid molecules having the described lengthsrefer to, e.g., at least about 15 contiguous nucleotides of thereference nucleic acid molecule. By stringent hybridization conditionsis intended overnight incubation at about 42° C. for about 2.5 hours in6×SSC/0.1% SDS, followed by washing of the filters four times for 15minutes in 1.0×SSC at 65° C., 0.1% SDS.

Fragments of the Hu-Asp encoding nucleic acid molecules describedherein, as well as polynucleotides capable of hybridizing to suchnucleic acid molecules may be used as a probe or as primers in apolymerase chain reaction (PCR). Such probes may be used, e.g., todetect the presence of Hu-Asp nucleic acids in in vitro assays, as wellas in Southern and northern blots. Cell types expressing Hu-Asp may alsobe identified by the use of such probes. Such procedures are well known,and the skilled artisan will be able to choose a probe of a lengthsuitable to the particular application. For PCR, 5′ and 3′ primerscorresponding to the termini of a desired Hu-Asp nucleic acid moleculeare employed to isolate and amplify that sequence using conventionaltechniques.

Other useful fragments of the Hu-Asp nucleic acid molecules areantisense or sense oligonucleotides comprising a single stranded nucleicacid sequence capable of binding to a target Hu-Asp mRNA (using a sensestrand), or Hu-Asp DNA (using an antisense strand) sequence. In apreferred embodiment of the invention these Hu-Asp antisenseoligonucleotides reduce Hu-Asp mRNA and consequent production of Hu-Asppolypeptides.

In another aspect, the invention includes Hu-Asp polypeptides with orwithout associated native pattern glycosylation. Both Hu-Asp1 andHu-Asp2 have canonical acceptor sites for Asn-linked sugars, withHu-Asp1 having two of such sites, and Hu-Asp2 having four. Hu-Aspexpressed in yeast or mammalian expression systems (discussed below) maybe similar to or significantly different from a native Hu-Asppolypeptide in molecular weight and glycosylation pattern. Expression ofHu-Asp in bacterial expression systems will provide non-glycosylatedHu-Asp.

The polypeptides of the present invention are preferably provided in anisolated form, and preferably are substantially purified. Hu-Asppolypeptides may be recovered and purified from tissues, cultured cells,or recombinant cell cultures by well-known methods, including ammoniumsulfate or ethanol precipitation, anion or cation exchangechromatography, phosphocellulose chromatography, hydrophobic interactionchromatography, affinity chromatography, hydroxylapatite chromatography,lectin chromatography, and high performance liquid chromatography(HPLC). In a preferred embodiment, an amino acid tag is added to theHu-Asp polypeptide using genetic engineering techniques that are wellknown to practitioners of the art which include addition of sixhistidine amino acid residues to allow purification by binding to nickelimmobilized on a suitable support, epitopes for polyclonal or monoclonalantibodies including but not limited to the T7 epitope, the myc epitope,and the V5a epitope, and fusion of Hu-Asp2 to suitable protein partnersincluding but not limited to glutathione-S-transferase or maltosebinding protein. In a preferred embodiment these additional amino acidsequences are added to the C-terminus of Hu-Asp but may be added to theN-terminus or at intervening positions within the Hu-Asp2 polypeptide.

The present invention also relates to vectors comprising thepolynucleotide molecules of the invention, as well as host celltransformed with such vectors. Any of the polynucleotide molecules ofthe invention may be joined to a vector, which generally includes aselectable marker and an origin of replication, for propagation in ahost. Because the invention also provides Hu-Asp polypeptides expressedfrom the polynucleotide molecules described above, vectors for theexpression of Hu-Asp are preferred. The vectors include DNA encoding anyof the Hu-Asp polypeptides described above or below, operably linked tosuitable transcriptional or translational regulatory sequences, such asthose derived from a mammalian, microbial, viral, or insect gene.Examples of regulatory sequences include transcriptional promoters,operators, or enhancers, mRNA ribosomal binding sites, and appropriatesequences which control transcription and translation. Nucleotidesequences are operably linked when the regulatory sequence functionallyrelates to the DNA encoding Hu-Asp. Thus, a promoter nucleotide sequenceis operably linked to a Hu-Asp DNA sequence if the promoter nucleotidesequence directs the transcription of the Hu-Asp sequence.

Selection of suitable vectors to be used for the cloning ofpolynucleotide molecules encoding Hu-Asp, or for the expression ofHu-Asp polypeptides, will of course depend upon the host cell in whichthe vector will be transformed, and, where applicable, the host cellfrom which the Hu-Asp polypeptide is to be expressed. Suitable hostcells for expression of Hu-Asp polypeptides include prokaryotes, yeast,and higher eukaryotic cells, each of which is discussed below.

The Hu-Asp polypeptides to be expressed in such host cells may also befusion proteins which include regions from heterologous proteins. Suchregions may be included to allow, e.g., secretion, improved stability,or facilitated purification of the polypeptide. For example, a sequenceencoding an appropriate signal peptide can be incorporated intoexpression vectors. A DNA sequence for a signal peptide (secretoryleader) may be fused inframe to the Hu-Asp sequence so that Hu-Asp istranslated as a fusion protein comprising the signal peptide. A signalpeptide that is functional in the intended host cell promotesextracellular secretion of the Hu-Asp polypeptide. Preferably, thesignal sequence will be cleaved from the Hu-Asp polypeptide uponsecretion of Hu-Asp from the cell. Nonlimiting examples of signalsequences that can be used in practicing the invention include the yeastIfactor and the honeybee melatin leader in sf9 insect cells.

In a preferred embodiment, the Hu-Asp polypeptide will be a fusionprotein which includes a heterologous region used to facilitatepurification of the polypeptide. Many of the available peptides used forsuch a function allow selective binding of the fusion protein to abinding partner. For example, the Hu-Asp polypeptide may be modified tocomprise a peptide to form a fusion protein which specifically binds toa binding partner, or peptide tag. Nonlimiting examples of such peptidetags include the 6-His tag, thioredoxin tag, hemaglutinin tag, GST tag,and OmpA signal sequence tag. As will be understood by one of skill inthe art, the binding partner which recognizes and binds to the peptidemay be any molecule or compound including metal ions (e.g., metalaffinity columns), antibodies, or fragments thereof, and any protein orpeptide which binds the peptide, such as the FLAG tag.

Suitable host cells for expression of Hu-Asp polypeptides includesprokaryotes, yeast, and higher eukaryotic cells. Suitable prokaryotichosts to be used for the expression of Hu-Asp include bacteria of thegenera Escherichia, Bacillus, and Salmonella, as well as members of thegenera Pseudomonas, Streptomyces, and Staphylococcus. For expression in,e.g., E. coli, a Hu-Asp polypeptide may include an N-terminal methionineresidue to facilitate expression of the recombinant polypeptide in aprokaryotic host. The N-terminal Met may optionally then be cleaved fromthe expressed Hu-Asp polypeptide. Other N-terminal amino acid residuescan be added to the Hu-Asp polypeptide to facilitate expression inEscherichia coli including but not limited to the T7 leader sequence,the T7-caspase 8 leader sequence, as well as others leaders includingtags for purification such as the 6-His tag (Example 9). Hu-Asppolypeptides expressed in E. coli may be shortened by removal of thecytoplasmic tail, the transmembrane domain, or the membrane proximalregion. Hu-Asp polypeptides expressed in E. coli may be obtained ineither a soluble form or as an insoluble form which may or may not bepresent as an inclusion body. The insoluble polypeptide may be renderedsoluble by guanidine HCl, urea or other protein denaturants, thenrefolded into a soluble form before or after purification by dilution ordialysis into a suitable aqueous buffer. If the inactive proform of theHu-Asp was produced using recombinant methods, it may be rendered activeby cleaving off the prosegment with a second suitable protease such ashuman immunodeficiency virus protease.

Expression vectors for use in prokaryotic hosts generally comprises oneor more phenotypic selectable marker genes. Such genes generally encode,e.g., a protein that confers antibiotic resistance or that supplies anauxotrophic requirement. A wide variety of such vectors are readilyavailable from commercial sources. Examples include pSPORT vectors, pGEMvectors (Promega), pPROEX vectors (LTI, Bethesda, Md.), Bluescriptvectors (Stratagene), pET vectors (Novagen) and pQE vectors (Qiagen).

Hu-Asp may also be expressed in yeast host cells from genera includingSaccharomyces, Pichia, and Kluveromyces. Preferred yeast hosts are S.cerevisiae and P. pastoris. Yeast vectors will often contain an originof replication sequence from a 2T yeast plasmid, an autonomouslyreplicating sequence (ARS), a promoter region, sequences forpolyadenylation, sequences for transcription termination, and aselectable marker gene. Vectors replicable in both yeast and E. coli(termed shuttle vectors) may also be used. In addition to theabove-mentioned features of yeast vectors, a shuttle vector will alsoinclude sequences for replication and selection in E. coli. Directsecretion of Hu-Asp polypeptides expressed in yeast hosts may beaccomplished by the inclusion of nucleotide sequence encoding the yeastI-factor leader sequence at the 5′ end of the Hu-Asp-encoding nucleotidesequence.

Insect host cell culture systems may also be used for the expression ofHu-Asp polypeptides. In a preferred embodiment, the Hu-Asp polypeptidesof the invention are expressed using an insect cell expression system(see Example 10). Additionally, a baculovirus expression system can beused for expression in insect cells as reviewed by Luckow and Summers,Bio/Technology 6:47 (1988).

In another preferred embodiment, the Hu-Asp polypeptide is expressed inmammalian host cells. Nonlimiting examples of suitable mammalian celllines include the COS7 line of monkey kidney cells (Gluzman et al., Cell23:175 (1981)), human embyonic kidney cell line 293, and Chinese hamsterovary (CHO) cells. Preferably, Chinese hamster ovary (CHO) cells areused for expression of Hu-Asp proteins (Example 11).

The choice of a suitable expression vector for expression of the Hu-Asppolypeptides of the invention will of course depend upon the specificmammalian host cell to be used, and is within the skill of the ordinaryartisan. Examples of suitable expression vectors include pcDNA3(Invitrogen) and pSVL (Pharmacia Biotech). A preferred vector forexpression of Hu-Asp polypeptides is pcDNA3.1-Hygro (Invitrogen).Expression vectors for use in mammalian host cells may includetranscriptional and translational control sequences derived from viralgenomes. Commonly used promoter sequences and enhancer sequences whichmay be used in the present invention include, but are not limited to,those derived from human cytomegalovirus (CMV), Adenovirus 2, Polyomavirus, and Simian virus 40 (SV40). Methods for the construction ofmammalian expression vectors are disclosed, for example, in Okayama andBerg (Mol. Cell. Biol. 3:280 (1983)); Cosman et al. (Mol. Immunol.23:935 (1986)); Cosman et al. (Nature 312:768 (1984)); EP-A-0367566; andWO 91/18982.

The polypeptides of the present invention may also be used to raisepolyclonal and monoclonal antibodies, which are useful in diagnosticassays for detecting Hu-Asp polypeptide expression. Such antibodies maybe prepared by conventional techniques. See, for example, Antibodies: ALaboratory Manual, Harlow and Land (eds.), Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, N.Y., (1988); Monoclonal Antibodies,Hybridomas: A New Dimension in Biological Analyses, Kennet et al.(eds.), Plenum Press, New York (1980). Synthetic peptides comprisingportions of Hu-Asp containing 5 to 20 amino acids may also be used forthe production of polyclonal or monoclonal antibodies after linkage to asuitable carrier protein including but not limited to keyhole limpethemacyanin (KLH), chicken ovalbumin, or bovine serum albumin usingvarious cross-linking reagents including carbodimides, glutaraldehyde,or if the peptide contains a cysteine, N-methylmaleimide. A preferredpeptide for immunization when conjugated to KLH contains the C-terminusof Hu-Asp1 or Hu-Asp2 comprising QRRPRDPEVVNDESSLVRHRWK (SEQ ID NO: 2,residues 497-518) or LRQQHDDFADDISLLK (SEQ ID NO:4, residues 486-501),respectively. See SEQ ID NOS: 33-34.

The Hu-Asp nucleic acid molecules of the present invention are alsovaluable for chromosome identification, as they can hybridize with aspecific location on a human chromosome. Hu-Asp1 has been localized tochromosome 21, while Hu-Asp2 has been localized to chromosome11q23.3-24.1. There is a current need for identifying particular siteson the chromosome, as few chromosome marking reagents based on actualsequence data (repeat polymorphisms) are presently available for markingchromosomal location. Once a sequence has been mapped to a precisechromosomal location, the physical position of the sequence on thechromosome can be correlated with genetic map data. The relationshipbetween genes and diseases that have been mapped to the same chromosomalregion can then be identified through linkage analysis, wherein thecoinheritance of physically adjacent genes is determined. Whether a geneappearing to be related to a particular disease is in fact the cause ofthe disease can then be determined by comparing the nucleic acidsequence between affected and unaffected individuals.

In another embodiment, the invention relates to a method of assayingHu-Asp function, specifically Hu-Asp2 function which involves incubatingin solution the Hu-Asp polypeptide with a suitable substrate includingbut not limited to a synthetic peptide containing the β-secretasecleavage site of APP, preferably one containing the mutation found in aSwedish kindred with inherited AD in which KM is changed to NL, suchpeptide comprising the sequence SEVNLDAEFR (SEQ ID NO: 63) in an acidicbuffering solution, preferably an acidic buffering solution of pH5.5(see Example 12) using cleavage of the peptide monitored by highperformance liquid chromatography as a measure of Hu-Asp proteolyticactivity. Preferred assays for proteolytic activity utilize internallyquenched peptide assay substrates. Such suitable substrates includepeptides which have attached a paired flurophore and quencher includingbut not limited to 7-amino-4-methyl coumarin and dinitrophenol,respectively, such that cleavage of the peptide by the Hu-Asp results inincreased fluorescence due to physical separation of the flurophore andquencher. Other paired flurophores and quenchers includebodipy-tetramethylrhodamine and QSY-5 (Molecular Probes, Inc.). In avariant of this assay, biotin or another suitable tag may be placed onone end of the peptide to anchor the peptide to a substrate assay plateand a flurophore may be placed at the other end of the peptide. Usefulflurophores include those listed above as well as Europium labels suchas W8044 (EG&g Wallac, Inc.). Cleavage of the peptide by Asp2 willrelease the flurophore or other tag from the plate, allowing compoundsto be assayed for inhibition of Asp2 proteolytic cleavage as shown by anincrease in retained fluorescence. Preferred colorimetric assays ofHu-Asp proteolytic activity utilize other suitable substrates thatinclude the P2 and P1 amino acids comprising the recognition site forcleavage linked to o-nitrophenol through an amide linkage, such thatcleavage by the Hu-Asp results in an increase in optical density afteraltering the assay buffer to alkaline pH.

In another embodiment, the invention relates to a method for theidentification of an agent that increases the activity of a Hu-Asppolypeptide selected from the group consisting of Hu-Asp1, Hu-Asp2(a),and Hu-Asp2(b), the method comprising

(a) determining the activity of said Hu-Asp polypeptide in the presenceof a test agent and in the absence of a test agent; and

(b) comparing the activity of said Hu-Asp polypeptide determined in thepresence of said test agent to the activity of said Hu-Asp polypeptidedetermined in the absence of said test agent;

whereby a higher level of activity in the presence of said test agentthan in the absence of said test agent indicates that said test agenthas increased the activity of said Hu-Asp polypeptide. Such tests can beperformed with Hu-Asp polypeptide in a cell free system and withcultured cells that express Hu-Asp as well as variants or isoformsthereof.

In another embodiment, the invention relates to a method for theidentification of an agent that decreases the activity of a Hu-Asppolypeptide selected from the group consisting of Hu-Asp1, Hu-Asp2(a),and Hu-Asp2(b), the method comprising

(a) determining the activity of said Hu-Asp polypeptide in the presenceof a test agent and in the absence of a test agent; and

(b) comparing the activity of said Hu-Asp polypeptide determined in thepresence of said test agent to the activity of said Hu-Asp polypeptidedetermined in the absence of said test agent;

whereby a lower level of activity in the presence of said test agentthan in the absence of said test agent indicates that said test agenthas decreased the activity of said Hu-Asp polypeptide. Such tests can beperformed with Hu-Asp polypeptide in a cell free system and withcultured cells that express Hu-Asp as well as variants or isoformsthereof.

In another embodiment, the invention relates to a novel cell line(HEK125.3 cells) for measuring processing of amyloid β peptide (Aβ) fromthe amyloid protein precursor (APP). The cells are stable transformantsof human embryonic kidney 293 cells (HEK293) with a bicistronic vectorderived from pIRES-EGFP (Clontech) containing a modified human APP cDNA,an internal ribosome entry site and an enhanced green fluorescentprotein (EGFP) cDNA in the second cistron. The APP cDNA was modified byadding two lysine codons to the carboxyl terminus of the APP codingsequence. This increases processing of Aβ peptide from human APP by 2-4fold. This level of Aβ peptide processing is 60 fold higher than is seenin nontransformed HEK293 cells. HEK125.3 cells will be useful for assaysof compounds that inhibit Aβ peptide processing. This invention alsoincludes addition of two lysine residues to the C-terminus of other APPisoforms including the 751 and 770 amino acid isoforms, to isoforms ofAPP having mutations found in human AD including the Swedish KM→NL andV717→F mutations, to C-terminal fragments of APP, such as thosebeginning with the β-secretase cleavage site, to C-terminal fragments ofAPP containing the β-secretase cleavage site which have been operablylinked to an N-terminal signal peptide for membrane insertion andsecretion, and to C-terminal fragments of APP which have been operablylinked to an N-terminal signal peptide for membrane insertion andsecretion and a reporter sequence including but not limited to greenfluorescent protein or alkaline phosphatase, such that β-secretasecleavage releases the reporter protein from the surface of cellsexpressing the polypeptide.

Having generally described the invention, the same will be more readilyunderstood by reference to the following examples, which are provided byway of illustration and are not intended as limiting.

EXAMPLE 1 Development of a Search Algorithm Useful for theIdentification of Aspartyl Proteases, and Identification of C. elegansAspartyl Protease Genes in Wormpep 12

Materials and Methods:

Classical aspartyl proteases such as pepsin and renin possess atwo-domain structure which folds to bring two aspartyl residues intoproximity within the active site. These are embedded in the shorttripeptide motif DTG, or more rarely, DSG. The DTG or DSG active sitemotif appears at about residue 25-30 in the enzyme, but at about 65-70in the proenzyme (prorenin, pepsinogen). This motif appears again about150-200 residues downstream. The proenzyme is activated by cleavage ofthe N-terminal prodomain. This pattern exemplifies the double domainstructure of the modern day aspartyl enzymes which apparently arose bygene duplication and divergence. Thus;NH₂—X-D²⁵TG-Y-D^(Y+25)TG-Cwhere X denotes the beginning of the enzyme, following the N-terminalprodomain, and Y denotes the center of the molecule where the generepeat begins again.

In the case of the retroviral enzymes such as the HIV protease, theyrepresent only a half of the two-domain structures of well-known enzymeslike pepsin, cathepsin D, renin, etc. They have no prosegment, but arecarved out of a polyprotein precursor containing the gag and polproteins of the virus. They can be represented by:NH2-D25TG -C100

This “monomer” only has about 100 aa, so is extremely parsimonious ascompared to the other aspartyl protease “dimers” which have of the orderof 330 or so aa, not counting the N-terminal prodomain.

The limited length of the eukaryotic aspartyl protease active site motifmakes it difficult to search EST collections for novel sequences. ESTsequences typically average 250 nucleotides, and so in this case wouldbe unlikely to span both aspartyl protease active site motifs. Instead,we turned to the C. elegans genome. The C. elegans genome is estimatedto contain around 13,000 genes. Of these, roughly 12,000 have beensequenced and the corresponding hypothetical open reading frame (ORF)has been placed in the database Wormpep 12. We used this database as thebasis for a whole genome scan of a higher eukaryote for novel aspartylproteases, using an algorithm that we developed specifically for thispurpose. The following AWK script for locating proteins containing twoDTG or DSG motifs was used for the search, which was repeated four timesto recover all pairwise combinations of the aspartyl motif.

BEGIN{RS=“>“} /* defines “>“ as record separator for FASTA format */ {pos = index($0,”DTG”) /*finds “DTG” in record*/ if (pos>0) { rest =substr($0,pos+3) /*get rest of record after first DTG*/ pos2 =index(rest,”DTG”) /*find second DTG*/ if (pos2>0) printf(“%s%s\n”,“>”,$0)} /*report hits*/ } }

The AWK script shown above was used to search Wormpep12, which wasdownloaded from ftp.sanger.ac.uk/pub/databases/wormpep, for sequenceentries containing at least two DTG or DSG motifs. Using AWK limitedeach record to 3000 characters or less. Thus, 35 or so larger recordswere eliminated manually from Wormpep 12 as in any case these wereunlikely to encode aspartyl proteases.

Results and Discussion:

The Wormpep 12 database contains 12,178 entries, although some of these(<10%) represent alternatively spliced transcripts from the same gene.Estimates of the number of genes encoded in the C. elegans genome is onthe order of 13,000 genes, so Wormpep12 may be estimated to covergreater than 90% of the C. elegans genome.

Eukaryotic aspartyl proteases contain a two-domain structure, probablyarising from ancestral gene duplication. Each domain contains the activesite motif D(S/T)G located from 20-25 amino acid residues into eachdomain. The retroviral (e.g., HIV protease) or retrotransposon proteasesare homodimers of subunits which are homologous to a single eukaryoticaspartyl protease domain. An AWK script was used to search the Wormpep12database for proteins in which the D(S/T)G motif occurred at leasttwice. This identified >60 proteins with two DTG or DSG motifs. Visualinspection was used to select proteins in which the position of theaspartyl domains was suggestive of a two-domain structure meeting thecriteria described above.

In addition, the PROSITE eukaryotic and viral aspartyl protease activesite pattern PS00141 was used to search Wormpep12 for candidate aspartylproteases. (Bairoch A., Bucher P., Hofmann K., The PROSITE database: itsstatus in 1997, Nucleic Acids Res. 24:217-221(1997)). This generated anoverlapping set of Wormpep12 sequences. Of these, seven sequencescontained two DTG or DSG motifs and the PROSITE aspartyl protease activesite pattern. Of these seven, three were found in the same cosmid clone(F21F8.3, F21F8.4, and F21F8.7) suggesting that they represent a familyof proteins that arose by ancestral gene duplication. Two other ORFswith extensive homology to F21F8.3, F21F8.4 and F21F8.7 are present inthe same gene cluster (F21F8.2 and F21F8.6), however, these contain onlya single DTG motif. Exhaustive BLAST searches with these seven sequencesagainst Wormpep12 failed to reveal additional candidate aspartylproteases in the C. elegans genome containing two repeats of the DTG orDSG motif.

BLASTX search with each C. elegans sequence against SWISS-PROT, GenPepand TREMBL revealed that R12H7.2 was the closest worm homologue to theknown mammalian aspartyl proteases, and that T18H9.2 was somewhat moredistantly related, while CEASP1, F21F8.3, F21F8.4, and F21F8.7 formed asubcluster which had the least sequence homology to the mammaliansequences.

Discussion:

APP, the presenilins, and p35, the activator of cdk5, all undergointracellular proteolytic processing at sites which conform to thesubstrate specificity of the HIV protease. Dysregulation of a cellularaspartyl protease with the same substrate specificity, might thereforeprovide a unifying mechanism for causation of the plaque and tanglepathologies in AD. Therefore, we sought to identify novel human aspartylproteases. A whole genome scan in C. elegans identified seven openreading frames that adhere to the aspartyl protease profile that we hadidentified. These seven aspartyl proteases probably comprise thecomplete complement of such proteases in a simple, multicellulareukaryote. These include four closely related aspartyl proteases uniqueto C. elegans which probably arose by duplication of an ancestral gene.The other three candidate aspartyl proteases (T18H9.2, R12H7.2 andC11D2.2) were found to have homology to mammalian gene sequences.

EXAMPLE 2 Identification of Novel Human Aspartyl Proteases UsingDatabase Mining by Genome Bridging

Materials and Methods:

Computer-assisted analysis of EST databases, cDNA, and predictedpolypeptide sequences:

Exhaustive homology searches of EST databases with the CEASP1, F21F8.3,F21F8.4, and F21F8.7 sequences failed to reveal any novel mammalianhomologues. TBLASTN searches with R12H7.2 showed homology to cathepsinD, cathepsin E, pepsinogen A, pepsinogen C and renin, particularlyaround the DTG motif within the active site, but also failed to identifyany additional novel mammalian aspartyl proteases. This indicates thatthe C. elegans genome probably contains only a single lysosomal aspartylprotease which in mammals is represented by a gene family that arosethrough duplication and consequent modification of an ancestral gene.

TBLASTN searches with T18H9.2, the remaining C. elegans sequence,identified several ESTs which assembled into a contig encoding a novelhuman aspartyl protease (Hu-ASP1). As is described above in Example 1,BLASTX search with the Hu-ASP1 contig against SWISS-PROT revealed thatthe active site motifs in the sequence aligned with the active sites ofother aspartyl proteases. Exhaustive, repetitive rounds of BLASTNsearches against LifeSeq, LifeSeqFL, and the public EST collectionsidentified 102 EST from multiple cDNA libraries that assembled into asingle contig. The 51 sequences in this contig found in public ESTcollections also have been assembled into a single contig (THC213329) byThe Institute for Genome Research (TIGR). The TIGR annotation indicatesthat they failed to find any hits in the database for the contig. Notethat the TIGR contig is the reverse complement of the LifeSeq contigthat we assembled. BLASTN search of Hu-ASP1 against the rat and mouseEST sequences in ZooSeq revealed one homologous EST in each database(Incyte clone 700311523 and IMAGE clone 313341, GenBank accession numberW10530, respectively).

TBLASTN searches with the assembled DNA sequence for Hu-ASP1 againstboth LifeSeqFL and the public EST databases identified a second, relatedhuman sequence (Hu-Asp2) represented by a single EST (2696295).Translation of this partial cDNA sequence reveals a single DTG motifwhich has homology to the active site motif of a bovine aspartylprotease, NM1.

BLAST searches, contig assemblies and multiple sequence alignments wereperformed using the bioinformatics tools provided with the LifeSeq,LifeSeqFL and LifeSeq Assembled databases from Incyte. Predicted proteinmotifs were identified using either the ProSite dictionary (Motifs inGCG 9) or the Pfam database.

Full-length cDNA cloning of Hu-Asp1

The open reading frame of C. elegans gene T18H9.2CE was used to queryIncyte LifeSeq and LifeSeq-FL databases and a single electronic assemblyreferred to as 1863920CE1 was detected. The 5′ most cDNA clone in thiscontig, 1863920, was obtained from Incyte and completely sequenced onboth strands. Translation of the open reading frame contained withinclone 1863920 revealed the presence of the duplicated aspartyl proteaseactive site motif (DTG/DSG) but the 5′ end was incomplete. The remainderof the Hu-Asp1 coding sequence was determined by 5′ Marathon RACEanalysis using a human placenta Marathon ready cDNA template (Clontech).A 3′-antisense oligonucleotide primer specific for the 5′ end of clone1863920 was paired with the 5′-sense primer specific for the Marathonready cDNA synthetic adaptor in the PCR. Specific PCR products weredirectly sequenced by cycle sequencing and the resulting sequenceassembled with the sequence of clone 1863920 to yield the completecoding sequence of Hu-Asp-1 (SEQ ID NO: 1).

Several interesting features are present in the primary amino acidsequence of HuAsp1 (FIGS. 1A-1B, SEQ ID NO: 2). The sequence contains asignal peptide (residues 1-20 in SEQ ID NO: 2), a pro-segment, and acatalytic domain containing two copies of the aspartyl protease activesite motif (DTG/DSG). The spacing between the first and second activesite motifs is about 200 residues which should correspond to theexpected size of a single, eukaryotic aspartyl protease domain. Moreinterestingly, the sequence contains a predicted transmembrane domain(residues 469-492 in SEQ ID NO: 2) near its C-terminus which suggeststhat the protease is anchored in the membrane. This feature is not foundin any other aspartyl protease.

Cloning of a Full-length Hu-Asp-2 cDNAs:

As is described above in Example 1, genome wide scan of theCaenorhabditis elegans database WormPep12 for putative aspartylproteases and subsequent mining of human EST databases revealed a humanortholog to the C. elegans gene T18H9.2 referred to as Hu-Asp1. Theassembled contig for Hu-Asp1 was used to query for human paralogs usingthe BLAST search tool in human EST databases and a single significantmatch (2696295CE1) with approximately 60% shared identity was found inthe LifeSeq FL database. Similar queries of either gb105PubEST or thefamily of human databases available from TIGR did not identify similarEST clones. cDNA clone 2696295, identified by single pass sequenceanalysis from a human uterus cDNA library, was obtained from Incyte andcompletely sequence on both strands. This clone contained an incomplete1266 bp open-reading frame that encoded a 422 amino acid polypeptide butlacked an initiator ATG on the 5′ end. Inspection of the predictedsequence revealed the presence of the duplicated aspartyl proteaseactive site motif DTG/DSG, separated by 194 amino acid residues.Subsequent queries of later releases of the LifeSeq EST databaseidentified an additional ESTs, sequenced from a human astrocyte cDNAlibrary (4386993), that appeared to contain additional 5′ sequencerelative to clone 2696295. Clone 4386993 was obtained from Incyte andcompletely sequenced on both strands. Comparative analysis of clone4386993 and clone 2696295 confirmed that clone 4386993 extended theopen-reading frame by 31 amino acid residues including two in-frametranslation initiation codons. Despite the presence of the two in-frameATGs, no in-frame stop codon was observed upstream of the ATG indicatingthat the 4386993 may not be full-length. Furthermore, alignment of thesequences of clones 2696295 and 4386993 revealed a 75 base pairinsertion in clone 2696295 relative to clone 4386993 that results in theinsertion of 25 additional amino acid residues in 2696295. The remainderof the Hu-Asp2 coding sequence was determined by 5′ Marathon RACEanalysis using a human hippocampus Marathon ready cDNA template(Clontech). A 3′-antisense oligonucleotide primer specific for theshared 5′-region of clones 2696295 and 4386993 was paired with the5′-sense primer specific for the Marathon ready cDNA synthetic adaptorin the PCR. Specific PCR products were directly sequenced by cyclesequencing and the resulting sequence assembled with the sequence ofclones 2696295 and 4386993 to yield the complete coding sequence ofHu-Asp2(a) (SEQ ID NO: 3) and Hu-Asp2(b) (SEQ ID NO: 5), respectively.

Several interesting features are present in the primary amino acidsequence of Hu-Asp2(a) (FIGS. 3A-3B and SEQ ID NO: 4) and Hu-Asp-2(b)(FIGS. 2A-2B, SEQ ID NO: 6). Both sequences contain a signal peptide(residues 1-21 in SEQ ID NO: 4 and SEQ ID NO: 6), a pro-segment, and acatalytic domain containing two copies of the aspartyl protease activesite motif (DTG/DSG). The spacing between the first and second activesite motifs is variable due to the 25 amino acid residue deletion inHu-Asp-2(b) and consists of 168-versus-194 amino acid residues, forHu-Asp2(b) and Hu-Asp-2(a), respectively. More interestingly, bothsequences contains a predicted transmembrane domain (residues 455-477 inSEQ ID NO: 4 and 430-452 in SEQ ID NO: 6) near their C-termini whichindicates that the protease is anchored in the membrane. This feature isnot found in any other aspartyl protease except Hu-Asp1.

EXAMPLE 3 Molecular Cloning of Mouse Asp2 cDNA and Genomic DNA.

Cloning and Characterization of Murine Asp2 cDNA.

The murine ortholog of Hu-Asp2 was cloned using a combination of cDNAlibrary screening, PCR, and genomic cloning. Approximately 500,000independent clones from a mouse brain cDNA library were screened using a³²P-labeled coding sequence probe prepared from Hu-Asp2. Replicatepositives were subjected to DNA sequence analysis and the longest cDNAcontained the entire 3′ untranslated region and 47 amino acids in thecoding region. PCR amplification of the same mouse brain cDNA librarywith an antisense oligonucleotide primer specific for the 5′-most cDNAsequence determined above and a sense primer specific for the 5′ regionof human Asp2 sequence followed by DNA sequence analysis gave anadditional 980 bp of the coding sequence. The remainder of the 5′sequence of murine Asp-2 was derived from genomic sequence (see below).

Isolation and Sequence Analysis of the Murine Asp-2 Gene.

A murine EST sequence encoding a portion of the traurine Asp2 cDNA wasidentified in the GenBank EST database using the BLAST search tool andthe Hu-Asp2 coding sequence as the query. Clone g3160898 displayed 88%shared identity to the human sequence over 352 bp. Oligonucleotideprimer pairs specific for this region of murine Asp2 were thensynthesized and used to amplify regions of the murine gene. Murinegenomic DNA, derived from strain 129/SvJ, was amplified in thc PCR (25cycles) using various primer sets specific for murine Asp2 and theproducts analyzed by agarose gel electrophoresis. The primer set Zoo-1and Zoo-4 amplified a 750 bp fragment that contained approximately 600bp of intron sequence based on comparison to the known cDNA sequence.This primer set was then used to screen a murine BAC library by PCR, asingle genomic clone was isolated and this cloned was confirmed containthe murine Asp2 gene by DNA sequence analysis. Shotgun DNA sequencing ofthis Asp2 genomic clone and comparison to the cDNA sequences of bothHu-Asp2 and the partial murine cDNA sequences defined the full-lengthsequence of murine Asp2 (SEQ ID NO: 7). The predicted amino acidsequence of murine Asp2 (SEQ ID NO: 8) showed 96.4% shared identity (GCGBestFit algorithm) with 18/501 amino acid residue substitutions comparedto the human sequence (FIG. 4). The proteolytic processing of murineAsp2(a) is believed to be analogous to the processing described abovefor human Asp2(a). In addition, a variant lacking amino acid residues190-214 of SEQ ID NO: 8 is specifically contemplated as a murine Asp2(b)polypeptide and is set out as SEQ ID NO: 73. All forms of rnurineAsp2(b) gene and protein are intended as aspects of the invention.

EXAMPLE 4 Tissue Distribution of Expression of Hu-Asp2 Transcripts

Materials and Methods:

The tissue distribution of expression of Hu-Asp-2 was determined usingmultiple tissue Northern blots obtained from Clontech (Palo Alto,Calif.). Incyte clone 2696295 in the vector pINCY was digested tocompletion with EcoRI/NotI and the 1.8 kb cDNA insert purified bypreparative agarose gel electrophoresis. This fragment was radiolabeledto a specific activity >1×10⁹ dpm/μg by random priming in the presenceof [α-³²P-dATP] (>3000 Ci/mmol, Amersham, Arlington Heights, Ill.) andKlenow fragment of DNA polymerase I. Nylon filters containing denatured,size fractionated poly A⁺ RNAs isolated from different human tissueswere hybridized with 2×10⁶ dpm/ml probe in ExpressHyb buffer (Clontech,Palo Alto, Calif.) for 1 hour at 68° C. and washed as recommended by themanufacture. Hybridization signals were visualized by autoradiographyusing BioMax XR film (Kodak, Rochester, N.Y.) with intensifying screensat −80° C.

Results and Discussion:

Limited information on the tissue distribution of expression of Hu-Asp-2transcripts was obtained from database analysis due to the relativelysmall number of ESTs detected using the methods described above (<5). Inan effort to gain further information on the expression of the Hu-Asp2gene, Northern analysis was employed to determine both the size(s) andabundance of Hu-Asp2 transcripts. PolyA⁺ RNAs isolated from a series ofperipheral tissues and brain regions were displayed on a solid supportfollowing separation under denaturing conditions and Hu-Asp2 transcriptswere visualized by high stringency hybridization to radiolabeled insertfrom clone 2696295. The 2696295 cDNA probe visualized a constellation oftranscripts that migrated with apparent sizes of 3.0 kb, 4.4 kb and 8.0kb with the latter two transcript being the most abundant.

Across the tissues surveyed, Hu-Asp2 transcripts were most abundant inpancreas and brain with lower but detectable levels observed in allother tissues examined except thymus and PBLs. Given the relativeabundance of Hu-Asp2 transcripts in brain, the regional expression inbrain regions was also established. A similar constellation oftranscript sizes were detected in all brain regions examined(cerebellum, cerebral cortex, occipital pole, frontal lobe, temporallobe and putamen) with the highest abundance in the medulla and spinalcord.

EXAMPLE 5 Northern Blot Detection of HuAsp-1 and HuAsp-2 Transcripts inHuman Cell Lines

A variety of human cell lines were tested for their ability to produceHu-Asp1 and Asp2 mRNA. Human embryonic kidney (HEK-293) cells, Africangreen monkey (Cos-7) cells, Chinese hamster ovary (CHO) cells, HELAcells, and the neuroblastoma cell line IMR-32 were all obtained from theATCC. Cells were cultured in DME containing 10% FCS except CHO cellswhich were maintained in α-MEM/10% FCS at 37° C. in 5% CO₂ until theywere near confluence. Washed monolayers of cells (3×10⁷) were lysed onthe dishes and poly A⁺ RNA extracted using the Qiagen Oligotex DirectmRNA kit. Samples containing 2 μg of poly A⁺ RNA from each cell linewere fractionated under denaturing conditions (glyoxal-treated),transferred to a solid nylon membrane support by capillary action, andtranscripts visualized by hybridization with random-primed labeled (³²P)coding sequence probes derived from either Hu-Asp1 or Hu-Asp2.Radioactive signals were detected by exposure to X-ray film and by imageanalysis with a PhosphorImager.

The Hu-Asp1 cDNA probe visualized a similar constellation of transcripts(2.6 kb and 3.5 kb) that were previously detected is human tissues. Therelative abundance determined by quantification of the radioactivesignal was Cos-7>HEK 292=HELA>IMR32.

The Hu-Asp2 cDNA probe also visualized a similar constellation oftranscripts compared to tissue (3.0 kb, 4.4 kb, and 8.0 kb) with thefollowing relative abundance; HEK 293>Cos 7>IMR32>HELA.

EXAMPLE 6 Modification of APP to Increase Aβ Processing for In VitroScreening

Human cell lines that process Aβ peptide from APP provide a means toscreen in cellular assays for inhibitors of β- and γ-secretase.Production and release of Aβ peptide into the culture supernatant ismonitored by an enzyme-linked immunosorbent assay (EIA). Althoughexpression of APP is widespread and both neural and non-neuronal celllines process and release Aβ peptide, levels of endogenous APPprocessing are low and difficult to detect by EIA. Aβ processing can beincreased by expressing in transformed cell lines mutations of APP thatenhance Aβ processing. We made the serendipitous observation thataddition of two lysine residues to the carboxyl terminus of APP695increases Aβ processing still further. This allowed us to create atransformed cell line that releases Aβ peptide into the culture mediumat the remarkable level of 20,000 pg/ml.

Materials and Methods

Materials:

Human embryonic kidney cell line 293 (HEK293 cells) were obtainedinternally. The vector pIRES-EGFP was purchased from Clontech.Oligonucleotides for mutation using the polymerase chain reaction (PCR)were purchased from Genosys. A plasmid containing human APP695 (SEQ IDNO: 9 and SEQ ID NO: 10) was obtained from Northwestern UniversityMedical School. This was subcloned into pSK (Stratagene) at the Not1site creating the plasmid pAPP695.

Mutagenesis Protocol:

The Swedish mutation (K670N, M671L) was introduced into pAPP695 usingthe Stratagene Quick Change Mutagenesis Kit to create the plasmidpAPP695NL (SEQ ID NO: 11 and SEQ ID NO: 12) To introduce a di-lysinemotif at the C-terminus of APP695, the forward primer #276 5′GACTGACCACTCGACCAGGTTC (SEQ ID NO: 47) was used with the “patch” primer#274 5′ CGAATTAAATTCCAGCACACTGGCTACTTCTTGTTCTGCATCTCAAAGAAC (SEQ ID NO:48) and the flanking primer #275 CGAATTAAATTCCAGCACACTGGCTA (SEQ ID NO:49) to modify the 3′ end of the APP695 cDNA (SEQ ID NO: 15 and SEQ IDNO: 16). This also added a BstX1 restriction site that will becompatible with the BstX1 site in the multiple cloning site ofpIRES-EGFP. PCR amplification was performed with a Clontech HF AdvantagecDNA PCR kit using the polymerase mix and buffers supplied by themanufacturer. For “patch” PCR, the patch primer was used at 1/20th themolar concentration of the flanking primers. PCR amplification productswere purified using a QIAquick PCR purification kit (Qiagen). Afterdigestion with restriction enzymes, products were separated on 0.8%agarose gels and then excised DNA fragments were purified using aQIAquick gel extraction kit (Qiagen).

To reassemble a modified APP695-Sw cDNA, the 5′ Not1-Bg12 fragment ofthe APP695-Sw cDNA and the 3′Bg12-BstX1 APP695 cDNA fragment obtained byPCR were ligated into pIRES-EGFP plasmid DNA opened at the Not1 andBstX1 sites. Ligations were performed for 5 minutes at room temperatureusing a Rapid DNA Ligation kit (Boehringer Mannheim) and transformedinto Library Efficiency DH5a Competent Cells (GibcoBRL LifeTechnologies). Bacterial colonies were screened for inserts by PCRamplification using primers #276 and #275. Plasmid DNA was purified formammalian cell transfection using a QIAprep Spin Miniprep kit (Qiagen).The construct obtained was designated pMG125.3 (APPSW-KK, SEQ ID NO: 17and SEQ ID NO: 18).

Mammalian Cell Transfection:

HEK293 cells for transfection were grown to 80% confluence in Dulbecco'smodified Eagle's medium (DMEM) with 10% fetal bovine serum.Cotransfections were performed using LipofectAmine (Gibco-BRL) with 3 μgpMG125.3 DNA and 9 μg pcDNA3.1 DNA per 10×10⁶ cells. Three daysposttransfection, cells were passaged into medium containing G418 at aconcentration of 400 μg/ml. After three days growth in selective medium,cells were sorted by their fluorescence.

Clonal Selection of 125.3 Cells by FACS:

Cell samples were analyzed on an EPICS Elite ESP flow cytometer(Coulter, Hialeah, Fla.) equipped with a 488 nm excitation line suppliedby an air-cooled argon laser. EGFP emission was measured through a 525nm band-pass filter and fluorescence intensity was displayed on a4-decade log scale after gating on viable cells as determined by forwardand right angle light scatter. Single green cells were separated intoeach well of one 96 well plate containing growth medium without G418.After a four day recovery period, G418 was added to the medium to afinal concentration of 400 μg/ml. After selection, 32% of the wellscontained expanding clones. Wells with clones were expanded from the 96well plate to a 24 well plate and then a 6 well plate with the fastestgrowing colonies chosen for expansion at each passage. The final cellline selected was the fastest growing of the final six passaged. Thisclone, designated 125.3, has been maintained in G418 at 400 μg/ml withpassage every four days into fresh medium. No loss of Aβ production ofEGFP fluorescence has been seen over 23 passages.

Aβ EIA Analysis (Double Antibody Sandwich ELISA for hAβ 1-40/42):

Cell culture supernatants harvested 48 hours after transfection wereanalyzed in a standard Aβ EIA as follows. Human Aβ 1-40 or 1-42 wasmeasured using monoclonal antibody (mAb) 6E10 (Senetek, St. Louis, Mo.)and biotinylated rabbit antiserum 162 or 164 (New York State Institutefor Basic Research, Staten Island, N.Y.) in a double antibody sandwichELISA. The capture antibody 6E10 is specific to an epitope present onthe N-terminal amino acid residues 1-16 of hAβ. The conjugated detectingantibodies 162 and 164 are specific for hAβ 1-40 and 1-42, respectively.Briefly, a Nunc Maxisorp 96 well immunoplate was coated with 100 μl/wellof mAb 6E10 (5 μg/ml) diluted in 0.1M carbonate-bicarbonate buffer, pH9.6 and incubated at 4° C. overnight. After washing the plate 3× with0.01M DPBS (Modified Dulbecco's Phosphate Buffered Saline (0.008M sodiumphosphate, 0.002M potassium phosphate, 0.14M sodium chloride, 0.01 Mpotassium chloride, pH 7.4) from Pierce, Rockford, Ill.) containing0.05% of Tween-20 (DPBST), the plate was blocked for 60 minutes with 200μl of 10% normal sheep serum (Sigma) in 0.01M DPBS to avoid non-specificbinding. Human Aβ 1-40 or 1-42 standards 100 μl/well (Bachem, Torrance,Calif.) diluted, from a 1 mg/ml stock solution in DMSO, in culturemedium was added after washing the plate, as well as 100 μl/well ofsample, e.g., conditioned medium of transfected cells.

The plate was incubated for 2 hours at room temperature and 4° C.overnight. The next day, after washing the plate, 100 μl/wellbiotinylated rabbit antiserum 162 1:400 or 164 1:50 diluted inDPBST+0.5% BSA was added and incubated at room temperature for 1 hour,15 minutes. Following washes, 100 μl/well neutravidin-horseradishperoxidase (Pierce, Rockford, Ill.) diluted 1:10,000 in DPBST wasapplied and incubated for 1 hour at room temperature. After the lastwashes 100 μl/well of o-phenylnediamine dihydrochloride (SigmaChemicals, St. Louis, Mo.) in 50 mM citric acid/100 mM sodium phosphatebuffer (Sigma Chemicals, St. Louis, Mo.), pH 5.0, was added as substrateand the color development was monitored at 450 nm in a kineticmicroplate reader for 20 minutes using Soft max Pro software. Allstandards and samples were run in triplicates. The samples withabsorbance values falling within the standard curve were extrapolatedfrom the standard curves using Soft max Pro software and expressed inpg/ml culture medium.

Results:

Addition of two lysine residues to the carboxyl terminus of APP695greatly increases Aβ processing in HEK293 cells as shown by transientexpression (Table 1). Addition of the di-lysine motif to APP695increases Aβ processing to that seen with the APP695 containing theSwedish mutation. Combining the di-lysine motif with the Swedishmutation further increases processing by an additional 2.8 fold.

Cotransformation of HEK293 cells with pMG125.3 and pcDNA3.1 allowed dualselection of transformed cells for G418 resistance and high levelexpression of EGFP. After clonal selection by FACS, the cell lineobtained, produces a remarkable 20,000 pg Aβ peptide per ml of culturemedium after growth for 36 hours in 24 well plates. Production of Aβpeptide under various growth conditions is summarized in Table 2.

TABLE 1 Release of Aβ peptide into the culture medium 48 hours aftertransient transfection of HEK293 cells with the indicated vectorscontaining wildtype or modified APP. Values tabulated are mean + SD andP-value for pairwise comparison using Student's t-test assuming unequalvariances. Aβ 1-40 peptide APP Construct (pg/ml) Fold Increase P-valuepIRES-EGFP vector 147 + 28 1.0 wt APP695 (142.3) 194 + 15 1.3 0.051 wtAPP695-KK (124.1) 424 + 34 2.8 3 × 10⁻⁵ APP695-Sw (143.3) 457 + 65 3.1 2× 10⁻³ APP695-SwKK (125.3) 1308 + 98  8.9 3 × 10⁻⁴

TABLE 2 Release of Aβ peptide from HEK125.3 cells under various growthconditions. Type of Culture Volume of Duration of Aβ 1-40 Aβ 1-42 PlateMedium Culture (pg/ml) (pg/ml) 24 well plate 400 μl 36 hr 28,036 1,439

EXAMPLE 7 Antisense Oligomer Inhibition of Abeta Processing in HEK125.3Cells

The sequences of Hu-Asp1 and Hu-Asp2 were provided to Sequitur, Inc(Natick, Mass.) for selection of targeted sequences and design of 2ndgeneration chimeric antisense oligomers using prorietary technology(Sequitur Ver. D Pat pending #3002). Antisense oligomers Lot# S644,S645, S646 and S647 were targeted against Asp1. Antisense oligomers Lot#S648, S649, S650 and S651 were targeted against Asp2. Control antisenseoligomers Lot# S652, S653, S655, and S674 were targeted against anirrelevant gene and antisense oligomers Lot #S656, S657, S658, and S659were targeted against a second irrelevant gene.

For transfection with the antisense oligomers, HEK125.3 cells were grownto about 50% confluence in 6 well plates in Minimal Essential Medium(MEM) supplemented with 10% fetal calf serum. A stock solution ofoligofectin G (Sequitur Inc., Natick, Mass.) at 2 mg/ml was diluted to50 μg/ml in serum free MEM. Separately, the antisense oligomer stocksolution at 100 μM was diluted to 800 nM in Opti-MEM (GIBCO-BRL, GrandIsland, N.Y.). The diluted stocks of oligofectin G and antisenseoligomer were then mixed at a ratio of 1:1 and incubated at roomtemperature. After 15 minutes incubation, the reagent was diluted 10fold into MEM containing 10% fetal calf serum and 2 ml was added to eachwell of the 6 well plate after first removing the old medium. Aftertransfection, cells were grown in the continual presence of theoligofectin G/antisense oligomer. To monitor Aβ peptide release, 400 μlof conditioned medium was removed periodically from the culture well andreplaced with fresh medium beginning 24 hours after transfection. Aβpeptides in the conditioned medium were assayed via immunoprecipitationand Western blotting. Data reported are from culture supernatantsharvested 48 hours after transfection.

The 16 different antisense oligomers obtained from Sequitur Inc. weretransfected separately into HEK125.3 cells to determine their affect onAβ peptide processing. Only antisense oligomers targeted against Asp2significantly reduced Abeta processing by HEK125.3 cells. Both Aβ (1-40)and Aβ (1-42) were inhibited by the same degree. In Table 3, percentinhibition is calculated with respect to untransfected cells. Antisenseoligomer reagents giving greater than 50% inhibition are marked with anasterisk. For ASP2, 4 of 4 antisense oligomers gave greater than 50%inhibition with an average inhibition of 62% for Aβ 1-40 processing and60% for Aβ 1-42 processing.

TABLE 3 Inhibition of Aβ peptide release from HEK125.3 cells treatedwith antisense oligomers. Gene Targeted Antisense Oligomer Abeta (1-40)Abeta (1-42) Asp2-1 S648 71%* 67%* Asp2-2 S649 83%* 76%* Asp2-3 S65046%* 50%* Asp2-4 S651 47%* 46%* Con1-1 S652 13% 18% Con1-2 S653 35% 30%Con1-3 S655  9% 18% Con1-4 S674 29% 18% Con2-1 S656 12% 18% Con2-2 S65716% 19% Con2-3 S658  8% 35% Con2-4 S659  3% 18%

Since HEK293 cells derive from kidney, the experiment was extended tohuman IMR-32 neuroblastoma cells which express all three APP isoformsand which release Aβ peptides into conditioned medium at measurablelevels. (See Neill et al., J. NeuroSci. Res., (1994) 39: 482-93; andAsami-Odaka et al., Biochem., (1995) 34:10272-8.) Essentially identicalresults were obtained in the neuroblastoma cells as the HEK293 cells. Asshown in Table 3B, the pair of Asp2 antisense oligomers reduced Asp2mRNA by roughly one-half, while the pair of reverse control oligomerslacked this effect (Table 3B).

TABLE 3B Reduction of Aβ40 and Aβ42 in human neuroblastoma IMR-32 cellsand mouse neuroblastoma Neuro-2A cells treated with Asp2 antisense andcontrol oligomers as indicated. Oligomers were transfected inquadruplicate cultures. Values tabulated are normalized against culturestreated with oligofectin-G ™ only (mean + SD, **p < 0.001 compared toreverse control oligomer). Asp2 IMR-32 cells Neuro-2A cells mRNA Aβ40Aβ42 Aβ40 Aβ42 Asp2-1A −75% −49 + 2%** −42 + 14%** −70 + 7%** −67 + 2%**Asp2-1R 0.16  −0 + 3% 21.26  −9 + 15% 1.05 Asp2-2A −39% −43 + 3%** −44 +18%** −61 + 12%** −61 + 12%** Asp2-2R 0.47 12.2 19.22 6.15  −8 + 10%

Together with the reduction in Asp2 mRNA there was a concomitantreduction in the release of Aβ40 and Aβ42 peptides into the conditionedmedium. Thus, Asp2 functions directly or indirectly in a human kidneyand a human neuroblastoma cell line to facilitate the processing of APPinto Aβ peptides. Molecular cloning of the mouse Asp2 cDNA revealed ahigh degree of homology to human (>96% amino acid identity, see Example3), and indeed, complete nucleotide identity at the sites targeted bythe Asp2-1A and Asp2-2A antisense oligomers. Similar results wereobtained in mouse Neuro-2a cells engineered to express APP-Sw-KK. TheAsp2 antisense oligomers reduced release of Aβ peptides into the mediumwhile the reverse control oligomers did not (Table 3B). Thus, the threeantisense experiments with HEK293, IMR-32 and Neuro-2a cells indicatethat Asp2 acts directly or indirectly to facilitate Aβ processing inboth somatic and neural cell lines.

EXAMPLE 8 Demonstration of Hu-Asp2 β-Secretase Activity in CulturedCells

Several mutations in APP associated with early onset Alzheimer's diseasehave been shown to alter Aβ peptide processing. These flank the N- andC-terminal cleavage sites that release Aβ from APP. These cleavage sitesare referred to as the β-secretase and γ-secretase cleavage sites,respectively. Cleavage of APP at the β-secretase site creates aC-terminal fragment of APP containing 99 amino acids of 11,145 daltonsmolecular weight. The Swedish KM→NL mutation immediately upstream of theβ-secretase cleavage site causes a general increase in production ofboth the 1-40 and 1-42 amino acid forms of Aβ peptide. The London VFmutation (V717→F in the APP770 isoform) has little effect on total Aβpeptide production, but appears to preferentially increase thepercentage of the longer 1-42 amino acid form of Aβ peptide by affectingthe choice of β-secretase cleavage site used during APP processing.Thus, we sought to determine if these mutations altered the amount andtype of Aβ peptide produced by cultured cells cotransfected with aconstruct directing expression of Hu-Asp2.

Two experiments were performed which demonstrate Hu-Asp2 β-secretaseactivity in cultured cells. In the first experiment, treatment ofHEK125.3 cells with antisense oligomers directed against Hu-Asp2transcripts as described in Example 7 was found to decrease the amountof the C-terminal fragment of APP created by β-secretase cleavage(CTF99) (FIG. 9). This shows that Hu-Asp2 acts directly or indirectly tofacilitate β-secretase cleavage. In the second experiment, increasedexpression of Hu-Asp2 in transfected mouse Neuro2A cells is shown toincrease accumulation of the CTF99 β-secretase cleavage fragment (FIG.10). This increase is seen most easily when a mutant APP-KK clonecontaining a C-terminal di-lysine motif is used for transfection. Afurther increase is seen when Hu-Asp2 is cotransfected with APP-Sw-KKcontaining the Swedish mutation KM→NL. The Swedish mutation is known toincrease cleavage of APP by the β-secretase.

A second set of experiments demonstrate Hu-Asp2 facilitates γ-secretaseactivity in cotransfection experiments with human embryonic kidneyHEK293 cells. Cotransfection of Hu-Asp2 with an APP-KK clone greatlyincreases production and release of soluble Aβ1-40 and Aβ1-42 peptidesfrom HEK293 cells. There is a proportionately greater increase in therelease of Aβ1-42. A further increase in production of Aβ1-42 is seenwhen Hu-Asp2 is cotransfected with APP-VF (SEQ ID NO: 13 and SEQ ID NO:14) or APP-VF-KK SEQ ID NO: 19 and SEQ ID NO: 20) clones containing theLondon mutation V717→F. The V717→F mutation is known to alter cleavagespecificity of the APP γ-secretase such that the preference for cleavageat the Aβ42 site is increased. Thus, Asp2 acts directly or indirectly tofacilitate γ-secretase processing of APP at the β42 cleavage site.

Materials

Antibodies 6E10 and 4G8 were purchased from Senetek (St. Louis, Mo.).Antibody 369 was obtained from the laboratory of Paul Greengard at theRockefeller University. Antibody C8 was obtained from the laboratory ofDennis Selkoe at the Harvard Medical School and Brigham and Women'sHospital.

APP Constructs Used

The APP constructs used for transfection experiments comprised thefollowing:

APP: wild-type APP695 (SEQ ID NOS: 9 & 10)

APP-Sw: APP695 containing the Swedish KM→NL mutation (SEQ ID NOS: 11 &12, wherein the lysine (K) at residue 595 of APP695 is changed toasparagine (N) and the methionine (M) at residue 596 of APP695 ischanged to leucine (L).),

APP-VF: APP695 containing the London V→F mutation (SEQ ID NOS: 13 & 14)(Affected residue 717 of the APP770 isoform corresponds with residue 642of the APP695 isoform. Thus, APP-VF as set in SEQ ID NO: 14 comprisesthe APP695 sequence, wherein the valine (V) at residue 642 is changed tophenylalanine (F).)

APP-KK: APP695 containing a C-terminal KK motif (SEQ ID NOS:. 15 & 16),

APP-Sw-KK: APP695-Sw containing a C-terminal KK motif (SEQ ID NOS: 17 &18),

APP-VF-KK: APP695-VF containing a C-terminal KK motif (SEQ ID NOS: 19 &20).

These were inserted into the vector pIRES-EGFP (Clontech, Palo AltoCalif.) between the Not1 and BstX1 sites using appropriate linkersequences introduced by PCR.

Transfection of Antisense Oligomers or Plasmid DNA Constructs in HEK293Cells, HEK125.3 Cells and Neuro-2A Cells,

Human embryonic kidney HEK293 cells and mouse Neuro-2a cells weretransfected with expression constructs using the Lipofectamine Plusreagent from Gibco/BRL. Cells were seeded in 24 well tissue cultureplates to a density of 70-80% confluence. Four wells per plate weretransfected with 2 μg DNA (3:1, APP:cotransfectant), 8 μl Plus reagent,and 4 μl Lipofectamine in OptiMEM. OptiMEM was added to a total volumeof 1 ml, distributed 200 μl per well and incubated 3 hours. Care wastaken to hold constant the ratios of the two plasmids used forcotransfection as well as the total amount of DNA used in thetransfection. The transfection media was replaced with DMEM, 10% FBS,NaPyruvate, with antibiotic/antimycotic and the cells were incubatedunder normal conditions (37° C., 5% CO₂) for 48 hours. The conditionedmedia were removed to polypropylene tubes and stored at −80° C. untilassayed for the content of Aβ1-40 and Aβ1-42 by EIA as described in thepreceding examples. Transfection of antisense oligomers into HEK125.3cells was as described in Example 7.

Preparation of Cell Extracts, Western Blot Protocol

Cells were harvested after being transfected with plasmid DNA for about60 hours. First, cells were transferred to 15-ml conical tube from theplate and centrifuged at 1,500 rpm for 5 minutes to remove the medium.The cell pellets were washed once with PBS. We then lysed the cells withlysis buffer (10 mM HEPES, pH 7.9, 150 mM NaCl; 10% glycerol, 1 mM EGTA,1 mM EDTA, 0.1 mM sodium vanadate and 1% NP-40). The lysed cell mixtureswere centrifuged at 5000 rpm and the supernatant was stored at −20° C.as the cell extracts. Equal amounts of extracts from HEK125.3 cellstransfected with the Asp2 antisense oligomers and controls wereprecipitated with antibody 369 that recognizes the C-terminus of APP andthen CTF99 was detected in the immunoprecipitate with antibody 6E10. Theexperiment was repeated using C8, a second precipitating antibody thatalso recognizes the C-terminus of APP. For Western blot of extracts frommouse Neuro-2a cells cotransfected with Hu-Asp2 and APP-KK, APP-Sw-KK,APP-VF-KK or APP-VF, equal amounts of cell extracts were electrophoresedthrough 4-10% or 10-20% Tricine gradient gels (NOVEX, San Diego,Calif.). Full length APP and the CTF99 β-secretase product were detectedwith antibody 6E10.

Results

Transfection of HEK125.3 cells with Asp2-1 or Asp2-2 antisense oligomersreduces production of the CTF β-secretase product in comparison to cellssimilarly transfected with control oligomers having the reverse sequence(Asp2-1 reverse & Asp2-2 reverse), see FIG. 9. Correspondingly,cotransfection of Hu-Asp2 into mouse Neuro-2a cells with the APP-KKconstruct increased the formation of CTF99. (See FIG. 10.) This wasfurther increased if Hu-Asp2 was coexpressed with APP-Sw-KK, a mutantform of APP containing the Swedish KM→NL mutation that increasesβ-secretase processing.

Effects of Asp2 on the production of Ab peptides from endogenouslyexpressed APP isoforms were assessed in HEK293 cells transfected with aconstruct expressing Asp2 or with the empty vector after selection oftransformants with the antibiotic G418. Aβ40 production was increased incells transformed with the Asp2 construct in comparison to thosetransformed with the empty vector DNA. Aβ40 levels in conditioned mediumcollected from the Asp2 transformed and control cultures was 424±45pg/ml and 113±58 pg/ml, respectively (p<0.001). Aβ42 release was belowthe limit of detection by the EIA, while the release of sAPPα wasunaffected, 112±8 ng/ml versus 111±40 ng/ml. This further indicates thatAsp2 acts directly or indirectly to facilitate the processing andrelease of Aβ from endogenously expressed APP.

Co-transfection of Hu-Asp2 with APP has little effect on Aβ40 productionbut increases Aβ42 production above background (Table 4). Addition ofthe di-lysine motif to the C-terminus of APP increases Aβ peptideprocessing about two fold, although Aβ40 and Aβ42 production remainquite low (352 pg/ml and 21 pg/ml, respectively). Cotransfection of Asp2with APP-KK further increases both Aβ40 and Aβ42 production.

The APP V717→F mutation has been shown to increase γ-secretaseprocessing at the Aβ42 cleavage site. Cotransfection of Hu-Asp2 with theAPP-VF or APP-VF-KK constructs increased Aβ42 production (a two foldincrease with APP-VF and a four-fold increase with APP-VF-KK, Table 4),but had mixed effects on Aβ40 production (a slight decrease with APP-VF,and a two fold increase with APP-VF-KK in comparison to the pcDNAcotransfection control. Thus, the effect of Asp2 on Aβ42 production wasproportionately greater leading to an increase in the ratio ofAβ42/total Ab. Indeed, the ratio of Aβ42/total Aβ reaches a very highvalue of 42% in HEK293 cells cotransfected with Hu-Asp2 and APP-VF-KK.

TABLE 4 Results of cotransfecting Hu-Asp2 or pcDNA plasmid DNA withvarious APP constructs containing the V717 → F mutation that modifiesγ-secretase processing. Cotransfection with Asp2 consistently increasesthe ratio of Aβ42/total Aβ. Values tabulated are Aβ peptide pg/ml. pcDNACotransfection Asp2 Cotransfection Aβ40 Aβ42 Aβ42/Total Aβ40 Aβ42Aβ42/Total APP 192 ± 18 <4   <2%  188 ± 40  8 ± 10  3.9% APP-VF 118 ± 1515 ± 19 11.5%  85 ± 7  24 ± 12 22.4% APP-KK 352 ± 24 21 ± 6  5.5% 1062 ±101 226 ± 49 17.5% APP-VF-KK 230 ± 31 88 ± 24 27.7%  491 ± 35 355 ± 36  42%

EXAMPLE 9 Bacterial Expression of Human Asp2(a)

Expression of Recombinant Hu-Asp2(a) in E. coli.

Hu-Asp2(a) can be expressed in E. coli after addition of N-terminalsequences such as a T7 tag (SEQ ID NOS: 21 and 22) or a T7 tag followedby a caspase 8 leader sequence (SEQ ID NOS: 23 and 24). Alternatively,reduction of the GC content of the 5′ sequence by site directedmutagenesis can be used to increase the yield of Hu-Asp2 (SEQ ID NOS: 25and 26). In addition, Asp2(a) can be engineered with a proteolyticcleavage site (SEQ ID NOS: 27 and 28). To produce a soluble proteinafter expression and refolding, deletion of the transmembrane domain andcytoplasmic tail, or deletion of the membrane proximal region,transmembrane domain, and cytoplasmic tail is preferred. Any materials(vectors, host cells, etc.) and methods described herein to expressHu-Asp2(a) should in principle be equally effective for expression ofHu-Asp2(b).

Methods

PCR with primers containing appropriate linker sequences was used toassemble fusions of Asp2(a) coding sequence with N-terminal sequencemodifications including a T7 tag (SEQ ID NOS: 21 and 22) or a T7-caspase8 leader (SEQ ID NOS: 23 and 24). These constructs were cloned into theexpression vector pet23a(+) [Novagen] in which a T7 promoter directsexpression of a T7 tag preceding a sequence of multiple cloning sites.To clone Hu-Asp2 sequences behind the T7 leader of pet23a+, thefollowing oligonucleotides were used for amplification of the selectedHu-Asp2(a) sequence: #553=GTGGATCCACCCAGCACGGCATCCGGCTG (SEQ ID NO: 35),#554=GAAAGCTTTCATGACTCATCTGTCTGTGGAATGTTG (SEQ ID NO: 36) which placedBamHI and HindIII sites flanking the 5′ and 3′ ends of the insert,respectively. The Asp2(a) sequence was amplified from the full lengthAsp2(a) cDNA cloned into pcDNA3.1 using the Advantage-GC cDNA PCR(Clontech) following the manufacturer's supplied protocol usingannealing & extension at 68° C. in a two-step PCR cycle for 25 cycles.The insert and vector were cut with BamHI and HindIII, purified byelectrophoresis through an agarose gel, then ligated using the Rapid DNALigation kit (Boerhinger Mannheim). The ligation reaction was used totransform the E. coli strain JM109 (Promega) and colonies were pickedfor the purification of plasmid (Qiagen, Qiaprep minispin) and DNAsequence analysis. For inducible expression using induction withisopropyl b-D-thiogalactopyranoside (IPTG), the expression vector wastransferred into E. coli strain BL21 (Stratagene). Bacterial cultureswere grown in LB broth in the presence of ampicillin at 100 μg/ml, andinduced in log phase growth at an OD600 of 0.6-1.0 with 1 mM IPTG for 4hour at 37° C. The cell pellet was harvested by centrifugation.

To clone Hu-Asp2 sequences behind the T7 tag and caspase leader (SEQ IDNOS: 23 and 24), the construct created above containing the T7-Hu-Asp2sequence (SEQ ID NOS: 21 and 22) was opened at the BamH1 site, and thenthe phosphorylated caspase 8 leader oligonucleotides#559=GATCGATGACTATCTCTGACTCTCCGCGTGAACAGGACG (SEQ ID NO: 37),#560=GATCCGTCCTGTTCACGCGGAGAGTCAGAGATAGTCATC (SEQ ID NO: 38) wereannealed and ligated to the vector DNA. The 5′ overhang for each set ofoligonucleotides was designed such that it allowed ligation into theBamHI site but not subsequent digestion with BamHI. The ligationreaction was transformed into JM109 as above for analysis of proteinexpression after transfer to E. coli strain BL21.

In order to reduce the GC content of the 5′ terminus of asp2(a), a pairof antiparallel oligos were designed to change degenerate codon bases in15 amino acid positions from G/C to A/T (SEQ ID NOS: 25 and 26). The newnucleotide sequence at the 5′ end of asp2 did not change the encodedamino acid and was chosen to optimize E. coli expression. The sequenceof the sense linker is 5′CGGCATCCGGCTGCCCCTGCGTAGCGGTCTGGGTGGTGCTCCACTGGGTCTGCGTCTGCCCCGGGAGACCGACGAA G 3′ (SEQ ID NO: 39). The sequence of theantisense linker is: 5′CTTCGTCGGTCTCCCGGGGCAGACGCAGACCCAGTGGAGCACCACCCAGACCGCTACGCAGGGGCAGCCGGATGCCG 3′ (SEQ ID NO: 40). After annealing thephosphorylated linkers together in 0.1 M NaCl-10 mM Tris, pH 7.4 theywere ligated into unique Cla I and Sma I sites in Hu-Asp2 in the vectorpTAC. For inducible expression using induction with isopropylb-D-thiogalactopyranoside (IPTG), bacterial cultures were grown in LBbroth in the presence of ampicillin at 100 μg/ml, and induced in logphase growth at an OD600 of 0.6-1.0 with 1 mM IPTG for 4 hour at 37° C.The cell pellet was harvested by centrifugation.

To create a vector in which the leader sequences can be removed bylimited proteolysis with caspase 8 such that this liberates a Hu-Asp2polypeptide beginning with the N-terminal sequence GSFV (SEQ ID NOS: 27and 28), the following procedure was followed. Two phosphorylatedoligonucleotides containing the caspase 8 cleavage site IETD, #571=5′GATCGATGACTATCTCTGACTCTCCGCTGGACTCTGGTATCGAAACCGACG (SEQ ID NO: 41) and#572=GATCCGTCGGTTTCGATACCAGAGTCCAGCGGAGAGTCAGAGATAGTCAT C (SEQ ID NO:42) were annealed and ligated into pET23a+ that had been opened withBamHI. After transformation into JM109, the purified vector DNA wasrecovered and orientation of the insert was confirmed by DNA sequenceanalysis.

The following oligonucleotides were used for amplification of theselected Hu-Asp2(a) sequence:

-   #573=5′AAGGATCCTTTGTGGAGATGGTGGACAACCTG, (SEQ ID NO: 43)-   #554=GAAAGCTTTCATGACTCATCTGTCTGTGGAATGTTG (SEQ ID NO: 44)    which placed BamHI and HindIII sites flanking the 5′ and 3′ ends of    the insert, respectively. The Hu-Asp2(a) sequence was amplified from    the full length Hu-Asp2(a) cDNA cloned into pcDNA3.1 using the    Advantage-GC cDNA PCR (Clontech) following the manufacturer's    supplied protocol using annealing & extension at 68° C. in a    two-step PCR cycle for 25 cycles. The insert and vector were cut    with BamHI and HindIII, purified by electrophoresis through an    agarose gel, then ligated using the Rapid DNA Ligation kit    (Boerhinger Mannheim). The ligation reaction was used to transform    the E. coli strain JM109 (Promega) and colonies were picked for the    purification of plasmid (Qiagen, Qiaprep minispin) and DNA sequence    analysis. For inducible expression using induction with isopropyl    b-D-thiogalactopyranoside (IPTG), the expression vector was    transferred into E. coli strain BL21 (Statagene). Bacterial cultures    were grown in LB broth in the presence of ampicillin at 100 μg/ml,    and induced in log phase growth at an OD600 of 0.6-1.0 with 1 mM    IPTG for 4 hour at 37° C. The cell pellet was harvested by    centrifugation.

To assist purification, a 6-His tag can be introduced into any of theabove constructs following the T7 leader by opening the construct at theBamHI site and then ligating in the annealed, phosphorylatedoligonucleotides containing the six histidine sequence#565=GATCGCATCATCACCATCACCATG (SEQ ID NO: 45),#566=GATCCATGGTGATGGTGATGATGC (SEQ ID NO: 46). The 5′ overhang for eachset of oligonucleotides was designed such that it allowed ligation intothe BamHI site but not subsequent digestion with BamHI.

Preparation of Bacterial Pellet:

36.34g of bacterial pellet representing 10.8L of growth was dispersedinto a total volume of 200 ml using a 20 mm tissue homogenizer probe at3000 to 5000 rpm in 2M KCl, 0.1M Tris, 0.05M EDTA, 1 mM DTT. Theconductivity adjusted to about 193 mMhos with water. After the pelletwas dispersed, an additional amount of the KCl solution was added,bringing the total volume to 500 ml. This suspension was homogenizedfurther for about 3 minutes at 5000 rpm using the same probe. Themixture was then passed through a Rannie high-pressure homogenizer at10,000 psi.

In all cases, the pellet material was carried forward, while the solublefraction was discarded. The resultant solution was centrifuged in a GSArotor for 1 hour at 12,500 rpm. The pellet was resuspended in the samesolution (without the DTT) using the same tissue homogenizer probe at2,000 rpm. After homogenizing for 5 minutes at 3000 rpm, the volume wasadjusted to 500 ml with the same solution, and spun for 1 hour at 12,500rpm. The pellet was then resuspended as before, but this time the finalvolume was adjusted to 1.5 L with the same solution prior tohomogenizing for 5 minutes. After centrifuging at the same speed for 30minutes, this procedure was repeated. The pellet was then resuspendedinto about 150 ml of cold water, pooling the pellets from the sixcentrifuge tubes used in the GSA rotor. The pellet has homogenized for 5minutes at 3,000 rpm, volume adjusted to 250 ml with cold water, thenspun for 30 minutes. Weight of the resultant pellet was 17.75 g.

Summary: Lysis of bacterial pellet in KCl solution, followed bycentrifugation in a GSA rotor was used to initially prepare the pellet.The same solution was then used an additional three times forresuspension/homogenization. A final water wash/homogenization was thenperformed to remove excess KCl and EDTA.

Solublization of Recombinant Hu-Asp2(a):

A ratio of 9-10 ml/gram of pellet was utilized for solubilizing therHuAsp2L from the pellet previously described. 17.75 g of pellet wasthawed, and 150 ml of 8M guanidine HCl, 5 mM βME, 0.1% DEA, was added.3M Tris was used. to titrate the pH to 8.6. The pellet was initiallyresuspended into the guanidine solution using a 20 mm tissue homogenizerprobe at 1000 rpm. The mixture was then stirred at 4° C. for 1 hourprior to centrifugation at 12,500 rpm for 1 hour in GSA rotor. Theresultant supernatant was then centrifuged for 30 minutes at 40,000×g inan SS-34 rotor. The final supernatant was then stored at −20° C., exceptfor 50 ml.

Immobilized Nickel Affinity Chromatography of Solubilized RecombinantHu-Asp2(a):

The following solutions were utilized:

A) 6M Guanidine HCl, 0.1 M NaP, pH 8.0, 0.01M Tris, 5 mM βME, 0.5 mMImidazole

A′) 6M Urea, 20 mM NaP, pH 6.80, 50 mM NaCl

B′) 6M Urea, 20 mM NaP, pH 6.20, 50 mM NaCl, 12 mM Imidazole

C′) 6M Urea, 20 mM NaP, pH 6.80, 50 mM NaCl, 300 mM Imidazole

Note: Buffers A′ and C′ were mixed at the appropriate ratios to giveintermediate concentrations of Imidazole.

The 50ml of solubilized material was combined with 50 ml of buffer Aprior to adding to 100-125 ml Qiagen Ni-NTA SuperFlow (pre-equilibratedwith buffer A) in a 5×10 cm Bio-Rad econo column. This was shaken gentlyovernight at 4° C. in the cold room.

Chromatography Steps:

Drained the resultant flow through.

Washed with 50 ml buffer A (collecting into flow through fraction)

Washed with 250 ml buffer A (wash 1)

Washed with 250 ml buffer A (wash 2)

Washed with 250 ml buffer A′

Washed with 250 ml buffer B′

Washed with 250 ml buffer A′

Eluted with 250 ml 75 mM Imidazole

Eluted with 250 ml 150 mM Imidazole (150-1)

Eluted with 250 ml 150 mM Imidazole (150-2)

Eluted with 250 ml 300 mM Imidazole (300-1)

Eluted with 250 ml 300 mM Imidazole (300-2)

Eluted with 250 ml 300 mM Imidazole (300-3)

Chromatography Results:

The Hu-Asp(a) eluted at 75 mM Imidazole through 300 mM Imidazole. The 75mM fraction, as well as the first 150 mM Imidazole (150-1) fractioncontained contaminating proteins as visualized on Coomassie Blue stainedgels. Therefore, fractions 150-2 and 300-1 will be utilized forrefolding experiments since they contained the greatest amount ofprotein as visualized on a Coomassie Blue stained gel.

Refolding Experiments of Recombinant Hu-Asp2(a):

Experiment 1:

Forty ml of 150-2 was spiked with 1M DTT, 3M Tris, pH 7.4 and DEA to afinal concentration of 6 mM, 50 mM, and 0.1% respectively. This wasdiluted suddenly (while stirring) with 200 ml of (4° C.) cold 20 mM NaP,pH 6.8, 150 mM NaCl. This dilution gave a final Urea concentration of1M. This solution remained clear, even if allowed to set open to the airat room temperature (RT) or at 4° C.

After setting open to the air for 4-5 hours at 4° C., this solution wasthen dialyzed overnight against 20 mM NaP, pH 7.4, 150 mM NaCl, 20%glycerol. This method effectively removes the urea in the solutionwithout precipitation of the protein.

Experiment 2:

Some of the 150-2 eluate was concentrated 2× on an Amicon Centriprep,10,000 MWCO, then treated as in Experiment 1. This material also stayedin solution, with no visible precipitation.

Experiment 3:

89 ml of the 150-2 eluate was spiked with 1M DTT, 3M Tris, pH 7.4 andDEA to a final concentration of 6 mM, 50 mM, and 0.1% respectively. Thiswas diluted suddenly (while stirring) with 445 ml of (4° C.) cold 20 mMNaP, pH 6.8, 150 mM NaCl. This solution appeared clear, with no apparentprecipitation. The solution was removed to RT and stirred for 10 minutesprior to adding MEA to a final concentration of 0.1 mM. This was stirredslowly at RT for 1 hour. Cystamine and CuSO4 were then added to finalconcentrations of 1 mM and 10 μM respectively. The solution was stirredslowly at RT for 10 minutes prior to being moved to the 4° C. cold roomand shaken slowly overnight, open to the air.

The following day, the solution (still clear, with no apparentprecipitation) was centrifuged at 100,000×g for 1 hour. Supernatantsfrom multiple runs were pooled, and the bulk of the stabilized proteinwas dialyzed against 20 mM NaP, pH 7.4, 150 mM NaCl, 20% glycerol. Afterdialysis, the material was stored at −20° C.

Some (about 10 ml) of the protein solution (still in 1M Urea) was savedback for biochemical analyses, and frozen at −20° C. for storage.

EXAMPLE 10 Expression of Hu-Asp2 and Derivatives in Insect Cells

Any materials (vectors, host cells, etc.) and methods that are useful toexpress Hu-Asp2(a) should in principle be equally effective forexpression of Hu-Asp2(b).

Expression by Baculovirus Infection.

The coding sequence of Hu-Asp2(a) and Hu-ASp2(b) and several derivativeswere engineered for expression in insect cells using the PCR. For thefull-length sequence, a 5′-sense oligonucleotide primer that modifiedthe translation initiation site to fit the Kozak consensus sequence waspaired with a 3′-antisense primer that contains the natural translationtermination codon in the Hu-Asp2 sequence. PCR amplification of thepcDNA3.1(hygro)/Hu-Asp2(a) template was used to prepare two derivativesof Hu-Asp2(a) or Hu-Asp(b) that delete the C-terminal transmembranedomain (SEQ ID NOS: 29-30 and 50-51, respectively) or delete thetransmembrane domain and introduce a hexa-histidine tag at theC-terminus (SEQ ID NOS: 31-32 and 52-53) respectively, were alsoengineered using PCR. The same 5′-sense oligonucleotide primer describedabove was paired with either a 3′-antisense primer that (1) introduced atranslation termination codon after codon 453 (SEQ ID NO: 3) or (2)incorporated a hexa-histidine tag followed by a translation terminationcodon in the PCR using pcDNA3.1(hygro)/Hu-Asp-2(a) as the template. Inall cases, the PCR reactions were performed amplified for 15 cyclesusing PwoI DNA polymerase (Boehringer-Mannheim) as outlined by thesupplier. The reaction products were digested to completion with BamHIand NotI and ligated to BamHI and NotI digested baculovirus transfervector pVL1393 (Invitrogen). A portion of the ligations was used totransform competent E. coli DH5_cells followed by antibiotic selectionon LB-Amp. Plasmid DNA was prepared by standard alkaline lysis andbanding in CsCl to yield the baculovirus transfer vectorspVL1393/Asp2(a), pVL1393/Asp2(a)ΔTM and pVL1393/Asp2(a)ΔTM(His)₆.Creation of recombinant baculoviruses and infection of sf9 insect cellswas performed using standard methods.

Expression by Transfection

Transient and stable expression of Hu-Asp2(a)ΔTM and Hu-Asp2(a)ΔTM(His)₆in High 5 insect cells was performed using the insect expression vectorpIZ/V5-His. The DNA inserts from the expression plasmids vectorspVL1393/Asp2(a), pVL1393/Asp2(a)ΔTM and pVL1393/Asp2(a)ΔTM(His)₆ wereexcised by double digestion with BamHI and NotI and subcloned into BamHIand NotI digested pIZ/V5-His using standard methods. The resultingexpression plasmids, referred to as pIZ/Hu-Asp2ΔTM andpIZ/Hu-Asp2ΔTM(His)₆, were prepared as described above.

For transfection, High 5 insect cells were cultured in High Five serumfree medium supplemented with 10 μg/ml gentamycin at 27° C. in sealedflasks. Transfections were performed using High five cells, High fiveserum free media supplemented with 10 μg/ml gentamycin, and InsectinPlusliposomes (Invitrogen, Carlsbad, Calif.) using standard methods.

For large scale transient transfections, 1.2×10⁷ high five cells wereplated in a 150 mm tissue culture dish and allowed to attach at roomtemperature for 15-30 minutes. During the attachment time theDNA/liposome mixture was prepared by mixing 6 ml of serum free media, 60μg Hu-Asp2(a)ΔTM/pIZ (+/−His) DNA and 120 μl of Insectin Plus andincubating at room temperature for 15 minutes. The plating media wasremoved from the dish of cells and replaced with the DNA/liposomemixture for 4 hours at room temperature with constant rocking at 2 rpm.An additional 6 ml of media was added to the dish prior to incubationfor 4 days at 27° C. in a humid incubator. Four days post transfectionthe media was harvested, clarified by centrifugation at 500×g, assayedfor Hu-Asp²(a) expression by Western blotting. For stable expression,the cells were treated with 50 μg/ml Zeocin and the surviving pool usedto prepared clonal cells by limiting dilution followed by analysis ofthe expression level as noted above.

Purification of Hu-Asp2(a)ΔTM and Hu-Asp2(a)ΔTM(His)₆

Removal of the transmembrane segment from Hu-Asp2(a) resulted in thesecretion of the polypeptide into the culture medium. Following proteinproduction by either baculovirus infection or transfection, theconditioned medium was harvested, clarified by centrifugation, anddialyzed against Tris-HCl (pH 8.0). This material was then purified bysuccessive chromatography by anion exchange (Tris-HCl, pH 8.0) followedby cation exchange chromatography (Acetate buffer at pH 4.5) using NaClgradients. The elution profile was monitored by (1) Western blotanalysis and (2) by activity assay using the peptide substrate describedin Example 12. For the Hu-Asp2(a)ΔTM(His)₆, the conditioned medium wasdialyzed against Tris buffer (pH 8.0) and purified by sequentialchromatography on IMAC resin followed by anion exchange chromatography.

Amino-terminal sequence analysis of the purified Hu-Asp2(a)ΔTM(His)₆protein revealed that the signal peptide had been cleaved (TQHGIRLPLR,corresponding to SEQ ID NO: 32, residues 22-3).

EXAMPLE 11 Expression of Hu-Asp2(a) and Hu-Asp(b) in CHO Cells

The materials (vectors, host cells, etc.) and methods described hereinfor expression of Hu-Asp2(a) are intended to be equally applicable forexpression of Hu-Asp2(b).

Heterologous Expression of Hu-Asp-2(a) in CHO-K1 Cells

The entire coding sequence of Hu-Asp2(a) was cloned into the mammalianexpression vector pcDNA3.1 (+)Hygro (Invitrogen, Carlsbad, Calif.) whichcontains the CMV immediate early promoter and bGH polyadenylation signalto drive over expression. The expression plasmid, pcDNA3.1(+)Hygro/Hu-Asp2(a), was prepared by alkaline lysis and banding in CsCland completely sequenced on both strands to verify the integrity of thecoding sequence.

Wild-type Chinese hamster ovary cells (CHO-K1) were obtained from theATCC. The cells were maintained in monolayer cultures in α-MEMcontaining 10% FCS at 37° C. in 5% CO₂. Two 100 mm dishes of CHO-K1cells (60% confluent) were transfected with pcDNA3.1(+)/Hygro alone(mock) or pcDNA3.1(+)Hygro/Hu-Asp2(a) or pcDNA3.1(+)Hygro/Hu-Asp2(b)using the cationic liposome DOTAP as recommended by the supplier (Roche,Indianapolis, Ind.). The cells were treated with-the plasmidDNA/liposome mixtures for 15 hours and then the medium replaced withgrowth medium containing 500 Units/ml hygromycin B. In the case ofpcDNA3.1(+)Hygro/Hu-Asp2(a) or (b) transfected CHO-K1 cells, individualhygromycin B-resistant cells were cloned by limiting dilution. Followingclonal expansion of the individual cell lines, expression of Hu-Asp2(a)or Hu-Asp2(b) protein was assessed by Western blot analysis using apolyclonal rabbit antiserum raised against recombinant Hu-Asp2 preparedby expression in E. coli. Near confluent dishes of each cell line wereharvested by scraping into PBS and the cells recovered bycentrifugation. The cell pellets were resuspended in cold lysis buffer(25 mM Tris-HCl (pH 8.0)/5 mM EDTA) containing protease inhibitors andthe cells lysed by sonication. The soluble and membrane fractions wereseparated by centrifugation (105,000×g, 60 min) and normalized amountsof protein from each fraction were then separated by SDS-PAGE. Followingelectrotransfer of the separated polypeptides to PVDF membranes,Hu-Asp-2(a) or Hu-Asp2(b) protein was detected using rabbit anti-Hu-Asp2antiserum ( 1/1000 dilution) and the antibody-antigen complexes werevisualized using alkaline phosphatase conjugated goat anti-rabbitantibodies ( 1/2500). A specific immunoreactive protein with an apparentMr value of 65 kDa was detected in pcDNA3.1(+)Hygro/Hu-Asp2 transfectedcells and not mock-transfected cells. Also, the Hu-Asp2 polypeptide wasonly detected in the membrane fraction, consistent with the presence ofa signal peptide and single transmembrane domain in the predictedsequence. Based on this analysis, clone #5 had the highest expressionlevel of Hu-Asp2(a) protein and this production cell lines was scaled upto provide material for purification.

Purification of Recombinant Hu-Asp-2(a) from CHO-K1/Hu-Asp2 Clone #5

In a typical purification, clone #5 cell pellets derived from 20 150 mmdishes of confluent cells, were used as the starting material. The cellpellets were resuspended in 50 ml cold lysis buffer as described above.The cells were lysed by polytron homogenization (2×20 sec) and thelysate centrifuged at 338,000×g for 20 minutes. The membrane pellet wasthen resuspended in 20 ml of cold lysis buffer containing 50 mMβ-octylglucoside followed by rocking at 4° C. for 1 hour. The detergentextract was clarified by centrifugation at 338,000×g for 20 minutes andthe supernatant taken for further analysis.

The β-octylglucoside extract was applied to a Mono Q anion exchangecolumn that was previously equilibrated with 25 mM Tris-HCl (pH 8.0)/50mM β-octylglucoside. Following sample application, the column was elutedwith a linear gradient of increasing NaCl concentration (0-1.0 M over 30minutes) and individual fractions assayed by Western blot analysis andfor β-secretase activity (see below). Fractions containing bothHu-Asp-2(a) immunoreactivity and β-secretase activity were pooled anddialyzed against 25 mM NaOAc (pH 4.5)/50 mM β-octylglucoside. Followingdialysis, precipitated material was removed by centrifugation and thesoluble material chromatographed on a MonoS cation exchange column thatwas previously equilibrated in 25 mM NaOAc (pH 4.5)/50 mMβ-octylglucoside. The column was eluted using a linear gradient ofincreasing NaCl concentration (0-1.0 M over 30 minutes) and individualfractions assayed by Western blot analysis and for β-secretase activity.Fractions containing both Hu-Asp2 immunoreactivity and β-secretaseactivity were combined and determined to be >95% pure bySDS-PAGE/Coomassie Blue staining.

The same methods were used to express and purify Hu-Asp2(b).

EXAMPLE 12 Assay of Hu-Asp2 β-Secretase Activity Using PeptideSubstrates

β-secretase Assay

Recombinant human Asp2(a) prepared in CHO cells and purified asdescribed in Example 11 was used to assay Asp2(a) proteolytic activitydirectly. Activity assays for Asp2(a) were performed using syntheticpeptide substrates containing either the wild-type APP β-secretase site(SEVKM↓DAEFR; SEQ ID NO: 64), the Swedish KM→NL mutation (SEVNL↓DAEFR;SEQ ID NO: 63), or the Aβ40 and 42 γ-secretase sites (RRGGVV↓IA↓TVIVGER;SEQ ID NO: 65). Reactions were performed in 50 mM2-[N-morpholino]ethane-sulfonate (“Na-MES,” pH 5.5) containing 1%β-octylglucoside, 70 mM peptide substrate, and recombinant Asp2(a) (1-5μg protein) for various times at 37° C. The reaction products werequantified by RP-HPLC using a linear gradient from 0-70 B over 30minutes (A=0.1% TFA in water, B=0.1% TFA/10% water/90% AcCN). Theelution profile was monitored by absorbance at 214 nm. In preliminaryexperiments, the two product peaks which eluted before the intactpeptide substrate, were confirmed to have the sequence DAEFR (SEQ ID NO:72) and SEVNL (SEQ ID NO: 73) using both Edman sequencing and MADLI-TOFmass spectrometry. Percent hydrolysis of the peptide substrate wascalculated by comparing the integrated peak areas for the two productpeptides and the starting material derived from the absorbance at 214nm. The sequence of cleavage/hydrolysis products was confirmed usingEdman sequencing and MADLI-TOF mass spectrometry.

The behavior of purified Asp2(a) in the proteolysis assays wasconsistent with the prior anti-sense studies which indicated thatAsp2(a) possesses β-secretase activity. Maximal proteolysis was seenwith the Swedigh β-secretase peptide, which, after 6 hours, was about10-fold higher than wild type APP.

The specificity of the protease cleavage reaction was determined byperforming the β-secretase assay in the presence of 8 μM pepstatin A andthe presence of a cocktail of protease inhibitors (10 μM leupeptin, 10μM E64, and 5 mM EDTA). Proteolytic activity was insensitive to both thepepstatin and the cocktail, which are inhibitors of cathepsin D (andother aspartyl proteases), serine proteases, cysteinyl proteases, andmetalloproteases, respectively.

Hu-Asp2(b) when similarly expressed in CHO cells and purified usingidentical conditions for extraction with β-o10ctylglucoside andsequential chromatography over Mono Q and Mono S also cleaves theSwedish β-secretase peptide in proteolysis assays using identical assayconditions.

Collectively, this data establishes that both forms of Asp2 (Hu-Asp2(a)and Hu-Asp2(b)) act directly in cell-free assays to cleave synthetic APPpeptides at the β-secretase site, and that the rate of cleavage isgreatly increased by the Swedish KM→NL mutation that is associated withAlzheimer's disease.

An alternative β-secretase assay utilizes internally quenchedfluorescent substrates to monitor enzyme activity using fluorescencespectroscopy in a single sample or multiwell format. Each reactioncontained 50 mM Na-MES (pH 5.5), peptide substrate MCA-EVKMDAEF[K-DNP](SEQ ID NO: 71; BioSource International) (50 μM) and purified Hu-Asp-2enzyme. These components were equilibrated to 37° C. for various timesand the reaction initiated by addition of substrate. Excitation wasperformed at 330 nm and the reaction kinetics were monitored bymeasuring the fluorescence emission at 390 nm. To detect compounds thatmodulate Hu-Asp-2 activity, the test compounds were added during thepreincubation phase of the reaction and the kinetics of the reactionmonitored as described above. Activators are scored as compounds thatincrease the rate of appearance of fluorescence while inhibitorsdecrease the rate of appearance of fluorescence.

It will be clear that the invention may be practiced otherwise than asparticularly described in the foregoing description and examples.

Numerous modifications and variations of the present invention arepossible in light of the above teachings and, therefore, are within thescope of the invention. The entire disclosure of all publications citedherein are hereby incorporated by reference.

1. A purified or isolated polypeptide comprising an amino acid sequenceat least 95% identical to a fragment of the aspartyl protease amino acidsequence set forth in FIG. 3 (SEQ ID NO: 4); wherein the fragmentincludes aspartyl protease active site tripeptides DTG and DSG andexhibits aspartyl protease activity involved in processing APP intoamyloid beta, wherein substitution differences between the amino acidsequence of the polypeptide and the amino acid sequence of the fragmentconsist of conservative substitutions, and wherein the polypeptideexhibits aspartyl protease activity involved in processing APP intoamyloid beta.
 2. A purified or isolated polypeptide according to claim 1wherein the polypeptide lacks a transmembrane domain.
 3. A purified orisolated polypeptide according to claim 1, wherein the polypeptidefurther comprises a heterologous peptide tag.
 4. A purified or isolatedpolypeptide comprising an amino acid sequence that is at least 95%identical to a fragment of the Asp2 protein amino acid sequence of SEQID NO: 4; wherein said fragment includes the aspartyl protease activesite tripeptides DTG and DSG and exhibits aspartyl protease activityinvolved in processing APP into amyloid beta; wherein said polypeptidelacks a transmembrane domain; and wherein said polypeptide exhibitsaspartyl protease activity involved in processing APP into amyloid beta.5. An isolated and purified polypeptide comprising the amino acidsequence set forth in SEQ ID NO: 4 or a fragment thereof, wherein thefragment includes aspartyl protease active site tripeptides DTG and DSGand exhibits aspartyl protease activity involved in processing APP intoamyloid beta.